Sutter Instrument dPatch Digital Patch Amplifier Operation Manual

Electrophysiology patch - clamp system with sutterpatch software

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dPatch

Digital Patch Amplifier

PATCH - CLAMP SYSTEM

SutterPatch

Operation Manual

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+1 415-883-0128

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+1 415-883-0572

ELECTROPHYSIOLOGY

WITH

SOFTWARE

One Digital Drive

Novato, CA 94949 USA

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Email:

www.sutter.com

info@sutter.com

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Page 1 dPatch ® Digital Patch Amplifier ELECTROPHYSIOLOGY PATCH - CLAMP SYSTEM WITH SutterPatch SOFTWARE ® Operation Manual One Digital Drive Novato, CA 94949 USA Voice: +1 415-883-0128 Web: www.sutter.com Fax: +1 415-883-0572 Email: info@sutter.com...
Page 2 Copyright © 2015 - 2022 Sutter Instrument Company. All Rights Reserved. dPatch , IPA , Double IPA and SutterPatch are registered trademarks of Sutter Instrument ® ® ® ® Company. All other product and company names are trademarks or registered trademarks ®...
Page 5: Safety Warnings And Precautions
Do not allow an unauthorized and/or untrained operative to use this instrument. Any misuse will be the sole responsibility of the user/owner, and Sutter Instrument Company assumes no implied or inferred liability for direct or consequential damages from this instru- ment if it is operated or used in any way other than for which it is designed.
Page 6: Operational
Other  Retain the original packaging for future transport of the instrument.  Sutter Instrument Company reserves the right to change specifications without prior notice.  Use of this instrument is for research purposes only. DPATCH – OPERATION MANUAL – REV. 2.3 (2022-10-24)
Page 7: Handling Micropipettes
Handling Micropipettes Failure to comply with any of the following precautions may result in injury to the users of this instrument as well as those working in the general area near the instrument.  The micropipettes used with this instrument are very sharp and relatively fragile. Avoid contact with micropipette tips to prevent accidentally impaling yourself.
Page 8: Table Of Contents
TABLE OF CONTENTS DISCLAIMER........................iii SAFETY WARNINGS AND PRECAUTIONS ............... iii Electrical..................................iii Operational ................................iv Other ..................................... iv Handling Micropipettes ............................. v 1. INTRODUCTION ......................1 1.1 Overview ................................1 1.2 Software Highlights ............................1 1.3 Experiment Structure ..........................2 2.
Page 9 4.1.1 Acquisition Control ................................... 72 4.1 Acquisition ............................... 72 4.1.2 Acquisition Measurements & Graphs ........................74 4.1.3 Acquisition: Routine Scope ..............................75 4.1.4 Camera Control ................................... 97 4.1.5 Free Run ......................................99 4.1.6 Membrane Test ..................................104 4.1.7 Paradigm Editor ..................................115 Amplifier ........................................
Page 10 viii Routine Editor: Routine Variables ..............................239 4.1.9 Solution Editor ..................................240 Template Editor ..................................... 243 4.2.1 Action Potential Analysis ..............................248 4.2 Data Analysis ...............................246 4.2.2 Analysis Editor ..................................254 4.2.3 Analysis Window ..................................261 4.2.4 Data Browser ....................................264 4.2.5 Data Navigator ..................................
Page 11 6. TROUBLESHOOTING ....................430 6.1 Technical Support.............................430 6.2 Manual ................................430 6.3.1 Error Messages and Notifications..........................430 6.3 Online Help................................430 6.4 Startup Issues ..............................431 6.5 Acquisition Issues .............................433 6.6 Analysis Issues ............................439 6.7 General Issues .............................440 APPENDIX A: Limited Warranty ................443 APPENDIX B: Software License .................
Page 12 Figure 2-10. Dashboard ........................18 Figure 2-11. Acquisition Dashboard....................18 Figure 3-1. Front of dPatch Cabinet ....................20 Figure 3-2. Rear of dPatch Cabinet ....................21 Figure 3-3. Amplifier Control Panels ....................29 Figure 3-4. Headstage Monitor ......................33 Figure 3-5.
Page 13 Figure 4-24. Paradigm Step: Hide Window ..................140 Figure 4-25. Paradigm Step: Scope Operation ................141 Figure 4-26. Paradigm Step: Set Axis ..................... 142 Figure 4-27. Paradigm Step: Checkbox................... 144 Figure 4-28. Paradigm Step: Set Mark ................... 145 Figure 4-29. Paradigm Step: Select Metadata Group ..............146 Figure 4-30.
Page 14 Figure 4-59. Waveform Editor ......................218 Figure 4-60. Template Waves ......................223 Figure 4-61. Real Time Measurement Settings ................231 Figure 4-62. Real Time Graphs ....................... 237 Figure 4-63. Routine Variables ......................239 Figure 4-64. Solution Editor ......................240 Figure 4-65. Template Editor ......................243 Figure 4-66.
Page 15 xiii Figure 4-94. Synaptic Event Analysis .................... 362 Figure 4-95. Command Window ..................... 367 Figure 4-96. Dashboard ........................368 Figure 4-97. Dashboard - Acquisition ..................... 371 Figure 4-98. Log Window ........................ 378 Figure 4-99. Notebook ........................387 Figure 4-100. Set Metadata Values ....................393 Figure 4-101.
Page 16 Table E-6. dPatch Headstage - Risetime ..................458 DPATCH – OPERATION MANUAL – REV. 2.3 (2022-10-24)
Page 17: Introduction
Its breakthrough digital design extends the limits of low-noise single-channel and whole-cell recording. Sutter Instrument Company is a leading manufacturer of innovative precision instrumentation in the neuroscience field. We have a worldwide reputation for the highest quality and perfor- mance of pipette pullers, micromanipulators, light and wavelength switchers.
Page 18: Experiment Structure
Convenient: All SutterPatch software is run by a single application. No need to launch multiple programs or to move data between programs. Comprehensive: All data recordings, analyses, graphs, layouts, configurations and con- trols are saved in a single experiment file. This ensures that data are always kept together with their complete contexts.
Page 19: Figure 1-1. Data Structure - Planned Paradigms
Figure 1-1. Data Structure - Planned Paradigms An Experiment with two “Planned” Paradigms running Routines. However, if a Routine is manually run, an “auto-triggered” Paradigm is created to maintain the Experiment structure. This default Paradigm ensures that each Series is associated with a Paradigm in the context of an Experiment.
Page 20 Routine Parameters: A Routine is the set of data acquisition and online data analysis parameters that control in- put and output channel timing, triggering, command waveforms, display and real-time anal- ysis. A loaded Routine “pool” file can contain multiple Routines for rapid access and execution. Series (Routine Data): Recording Routine data creates a Series composed of all sweeps of data from all input sig- nals.
Page 21: Table 1-1. Software Terminology
Segment: A Segment is a user-defined section of the command waveform. Each Segment has a wave- form type, amplitude and duration. SutterPatch Metadata: Metadata are additional information associated with stored data. These can include such information as the preparation (cell, tissue, animal), instrumentation (hardware, software), environmental parameters (temperature, atmospheric composition), stimuli (chemical com- pounds, light, acoustic), and other parameters.
Page 22: Installation
2. INSTALLATION 2.1 Computer Requirements Minimum Configuration OS (Operating System): Windows: Version 10 (64-bit versions) Most language packs are compatible. ( listed in OS: Control Panel > System ) macOS: Version 10.11 (El Capitan) to 10.15 (Cata- lina) ( listed in OS: Apple > About this Mac ) Virtual machines and OS emulators, such as Parallels and VMWare Fusion, are not supported.
Page 23: Sutterpatch System Environment
Also, sometimes BIOS settings, virus scanners and/or Windows updates can put a USB port to sleep. (See Troubleshooting: Startup Q&A ‘USB Communication Fails’.) Recommended Configuration ( for Bandwidths > 50 kHz ) CPU: As fast and powerful as possible. Note: Mac computers based on the Apple Silicon M1 ar- chitecture are not yet fully supported by Igor Pro.
Page 24: Mounting Instructions
• Extensibility via C and C++ modules. • Extensive online Help and PDF manual. 2.3 Mounting Instructions Rack Mounting: The dPatch amplifier is ready for mounting in a standard 19” wide equipment rack in a 2U space. A rack-mount hardware kit consisting of hex screws, washers and cage nuts is included.
Page 25: Install Software
1. Plug the female end of the power cord into the dPatch rear panel power receptacle. 2. Plug the male end of the included power cord into a grounded electrical mains outlet. 3. Push the dPatch power button to OFF (unlit position). WARNING! Hot-swapping of headstages should be avoided, or a software crash with data loss may occur.
Page 26 The SutterPatch ‘Release Notes’ PDF file for recent fixes and changes to the software is also found here. B. Choose Installer File Windows Full: SP + Igor 9 Full: SP + Igor 9 Full: SP + Igor 8 Full: SP + Igor 8 Updater: SP (Igor 9) Updater: SP (Igor 8) Separate “Full”...
Page 27 C. Install the Software Warning! Before launching the installer, make sure that SutterPatch is not run- ning, or file version errors will occur, and require a re-install. Use your file browser to navigate to the downloaded installer file and run it. 1.
Page 28: Install Model Cell
Applications/SutterPatch2/SP_Drivers/ (XOP) 4. Launch Igor Pro by clicking on its icon: 5. Activate its license as instructed. You will need to enter the Igor Pro 9 Serial Number and Activation Key found in your printed dPatch Quick Start Guide. 6. “Eject” the flash drive - wait for the “Safe to Remove Hardware” prompt, and then unplug it from the computer.
Page 29: Figure 2-3. Igor Pro Splash Screen
Figure 2-3. Igor Pro Splash Screen. Then the ‘Welcome to SutterPatch’ screen displays with launch options: Figure 2-4. Welcome Screen Igor Only Run Igor Pro (without launching SutterPatch). • Open Launch SutterPatch from a saved Experiment file. • Start Launch SutterPatch for a new Experiment. •...
Page 30: Figure 2-5. Emulation Modes
4. Next, the Igor Pro Command window opens. Then, if the dPatch amplifier is OFF or disconnected from the computer, the ‘No USB Connection’ dialog allows you to re-establish the USB connection, or to select a hardware-emulation mode: Figure 2-5. Emulation Modes. a.
Page 31: Figure 2-7. Dashboard
Major Preferences as set in the “SutterPatch” menu, entry “Set Preferences”: Configuration pool: not used Selected amplifier: dPatch Automatic experiment naming is ON: <pathname> Save data to separate HDF5 file is OFF Save entire experiment after each routine Warn when file size exceeds limit of 500 MB Maximal sweeps displayed in persistence display during acquisition: 30 Maximal sweeps displayed in persistence display during reanalysis: 30 Show event tags in reanalysis scope: ON...
Page 32: Figure 2-8. Acquisition Dashboard
Figure 2-8. Acquisition Dashboard. 8. Click on the ‘Control Panel’ icon, and the dPatch Control Panel’ is displayed: DPATCH – OPERATION MANUAL – REV. 2.3 (2022-10-24)
Page 33: Run A Membrane Test
Figure 2-9. dPatch Control Panel a. If “DEMO” displays in the dPatch Control Panel title bar, you are running in a hardware emulation mode. To run the physical instrument, ensure that the amplifier is powered on and its USB 3.0 cable is connected, then choose "New Experiment"...
Page 34: Figure 2-10. Dashboard
1. Go to the Dashboard window and click on the ‘Acquire Data’ icon. Figure 2-10. Dashboard 2. Click on the ‘Membrane Test’ icon. Figure 2-11. Acquisition Dashboard. The following test values assume a 5 kHz filter. 3. Test the BATH mode: This mode simulates placing an electrode into the bath solution and sending a voltage pulse through the solution.
Page 35 4. Test the SEAL mode: This mode simulates an electrode making contact onto a cell and forming a high-resistance gigaohm seal with the membrane. a. Set the Model Cell switch: Seal b. Click on the Membrane Test ‘Seal’ button. c. Verify value: Seal Resistance: ~1 GΩ...
Page 36: Hardware Operation
3. HARDWARE OPERATION 3.1 dPatch Front Panel The front panel of the dPatch system is used for the headstages, external I/O connections, and a power button. Figure 3-1. Front of dPatch Cabinet The front panel, from left to right: HEADSTAGE 1 & 2: HDMI-style Type A For dPatch headstages.
Page 37: Dpatch Rear Panel
3.2 dPatch Rear Panel The rear panel of the dPatch system is used for grounding, USB connections, and signal I/O. Figure 3-2. Rear of dPatch Cabinet [ Unlabeled ]: Power-entry receptacle For AC power cord. SIGNAL GROUND: 4 mm Banana socket Low-voltage grounding.
Page 38: Headstage
For a properly grounded laboratory, an electrical connection is needed from your laboratory’s electrical system to an “earth” ground. If your building’s electrical grid does not provide a good earth ground, you can create your own earth ground by making use of the building’s plumbing system, or by inserting a heavy metal bar deep into the earth.
Page 39 WARNING! Running a headstage in a “no load” open-circuit configuration for prolonged periods of time ([old: 1/2 hr, new: 2 hrs) in current- clamp mode should be avoided – headstage damage can occur from overheating. A 1 mm gold pin signal-ground socket is on the back of the headstage. One or two dPatch headstages can be attached in any order to either HEADSTAGE port.
Page 40: Holder
The frequency of automatic resets is proportional to the amount of current (amplitude) in the recorded signal. As the capacitor rating is 1 pF, a current of 1 pA will cause the reset to occur after 700 ms (when the capacitor reaches 70% of its maximal charge.) 2) “Resistive”...
Page 41: Assembly
3.5.1 Assembly The holder is assembled from 8 parts incorporated into a main barrel: End Cap – Gasket – Silver Wire – Barrel – Tubing – Gold Pin – Pin Cap - Lockdown Ring Barrel + Tubing Suction Tube Lockdown Ring + Pin Cap End Cap + Gasket Silver Wire Gold Pin...
Page 42: Chloriding Silver Wire
8. Insert the gold pin into the recessed end of the pin cap - push it through the pin hole until it stops. 9. Screw the pin cap onto the barrel so that pressure from the compressed snippet of tubing ensures good electrical contact between the silver wire and the gold pin. For the most stable configuration, before screwing the pin cap onto the barrel, solder the crimped silver wire to the end of the gold pin.
Page 43: Holder Maintenance
5. Dry for storage. Electrochemical Method 1. If needed, use a razor blade or fine sandpaper to rub off any insulation. 2. Optionally clean the silver (Ag) wire with ETOH (ethanol) to remove finger oils. 3. Connect a separate silver wire to each pole (positive and negative) of a household battery (1.5 V –...
Page 44: Dpatch Amplifier Control Panel
Caution! Washing with soapy water can leave a film. Continual cleaning with ethanol can degrade the polycarbonate parts. Do not clean with methanol or strong organic solvents such as acetone. 2. Blot dry. Weekly Cleaning: 1. At least once per week, disassemble holder. 2.
Page 45: General Controls
Figure 3-3. Amplifier Control Panels General Controls [ Headstage # ] tabs [ 1 – 2 ] For multiple headstages, each headstage maintains its own settings. Clicking on a headstage tab will open its last-used active mode (VC, CC) set- tings;...
Page 46 I meter: Displays the Current input channel level. VC button: Switches the dPatch amplifier from Current Clamp to Voltage Clamp mode. CC button: Switches the dPatch amplifier from Voltage Clamp to Current Clamp mode. If Dynamic Clamp is also active, the ‘CC’...
Page 47 Feedback Mode [ Range ] Two headstage-feedback modes are provided to improve recording performance under different conditions: capacitive mode for very-low-noise (single-channel) voltage-clamp recordings, and resistor mode for whole-cell voltage- and current-clamp recordings. For resistor mode, two whole-cell feedback resistors provide both regular and extended range current-clamp current-injection amplitudes.
Page 48 For Routines that contain inter-sweep intervals, if the headstage capacitor is reset during this interval, there is no interference with the acquired data. Such capacitor resets can also be forced by running the Par- adigm step ‘Amplifier / Reset Cap’. Note: The Virtual Input Channel ‘Integrator Reset’...
Page 49: Figure 3-4. Headstage Monitor
V-filter Default mode: Initiate with a mouse right-click or Shift-click. • Reset all fields to default settings, except: Liquid junction Offset value VC mode V-holding value CC mode Subtract Pipette Offset Show / Hide Controls The vertical ‘Show / Hide’ button displays/hides all controls (general and tabbed) below this button.
Page 50 In CC mode, the Auto Offset calibration can take up to 10 s for settling time. Allow Filter Bandwidth higher than 50 kHz When disabled, the input bandwidth is limited to 50 kHz or less. This restriction against very high throughput levels helps prevent inadvertently overloading the system resources during data acquisition and analysis.
Page 51 Equation Allows scaling and offsets to be applied. [ List ] Not assigned • Bath Temperature • Ambient Temperature • Atmospheric Pressure • Samples to Average [ 1, 2, 5, 10, 20. 50 ] Check Check for errors in the active equations and labels.
Page 52 Displays to the right of the Filter field. Show Gentle Switch Displays below the Filter field. Allows control of VC   CC mode switching. Reset Liquid Junction Values on Startup Resets the Control Panel ‘Liquid junction’ value to zero for new Experiments. --------------------------- [ Demo mode only ] Enable Headstage 1...
Page 53 Noise_On Liquid junction [ ±250.0 mV ] Enter a pre-calculated Liquid Junction Potential (LJP) value for the bath and micropipette solutions in use. This value is used by ‘Auto Offset’ to apply “online” LJP correction for whole-cell experiments. A liquid-liquid junction offset occurs when an “open” micropipette is placed into the bath, and an ionic potential forms between the two dissimilar solutions in the bath and micropipette.
Page 54: Figure 3-5. Vc Control Panel
The “Offset” field is to the right of the ‘Lock’ button, and is independent of the holding potential. “Auto” Use An ‘Auto Offset’ automatically populates this field with the hardware offset portion of the system offset. “Manual” Use Use for manual tuning of the amplifier.. Place an “open”...
Page 55 V-holding (mV) [ ±750.0 ] After achieving a seal, the holding voltage is typically set to the cell’s equilibrium or “resting” membrane potential (typically -60 to -80 mV for neurons.) This control is active during acquisition - changes are applied to the next sweep.
Page 56 Tip: For experiments where the shape of the response is of interest, an input filter rate of 10 kHz is commonly used. However, for very long stimuli, you might want to use a lower input filter rate. Note: Filtering is not applied in Demo mode; demo data uses the Routine Editor / Acquisition &...
Page 57 Cell Compensation Enable whole-cell capacitance compensation. Series Resistance [ 0.10 – 100.00 MΩ ] Membrane Capacitance [ 1.00 – 500.00 pF ] Opens a 2-D slider panel for simultaneous tuning of both parameters. Alert! When dragging with a mouse, slow down when approaching panel boundaries, else overshoot or undershoot of the values can occur.
Page 58 separately ] Pred [ 0 – 99% ] Prediction [ displays if enabled in dPatch Settings menu ] Lag: [ 1 – 100 µs ] (RC filter component) (see the Algorithms Appendix) Control the speed of the Correction while avoiding possible oscillations. Opens a 2-D slider panel for simultaneous tuning of both parameters.
Page 59: Figure 3-6. Cc Control Panel
Current Clamp Controls Figure 3-6. CC Control Panel The ‘CC’ tab displays the amplifier Current Clamp controls: I-holding: [ ±20,000 pA, ±200,000 pA ] A holding current can be preset here. The maximum range is set by the feedback ‘Range’ field below the VC and CC monitors.
Page 60 dPatch headstages have a fixed hardware sampling rate of 5 MHz. The actual system sampling rate is based on downsampling the hardware sampling rate, to the sampling value calculated by applying the Routine Editor / Input Channels Nyquist Factor to the selected filter Bandwidth. When recording from a Routine, either the Control Panel V-Filter setting or the Routine Editor / Input Channels / Filter Bandwidth setting can be used.
Page 61 Enable Bridge Balance Correction to remove voltage-drop effects from the electrode Series resistance. This occurs when command currents flow into the preparation, and voltage readings from the cell during the current flow (in- jection) are corrected. If you are simply recording voltage (I=0) without any current injection, then Bridge Balance can be ignored or left disabled.
Page 62 anytime to reset the scaling factor. [ the following controls only display if ‘Auto Bridge Balance’ is enabled in the ‘dPatch Settings’ menu ] Auto The Bridge Balance ‘Auto’ button can be used to approximate the correction value. For larger steps, it is recommended to run the ‘Auto’ function twice in a row.
Page 63: Figure 3-7. Dynamic Clamp Control Panel
When Dynamic Holding is enabled, the Holding Current is automatically disabled, as the current output is dynamically adjusted by the system If the amplifier is accidentally disconnected, then when the USB connection is reconnected, Dynamic Holding will be disabled. Dynamic Clamp Controls The dPatch system can be setup to perform full dynamic-clamp experiments.
Page 64 The Dynamic Clamp “Conductance Pool” name. Model [ #1 – 99 ] The model type. Mode The active acquisition mode. During Sweeps • Run Continuously • Update Rate [ 1, 2, 5, 10, 20, 50, 100, 200, 250, 500 kHz ] Voltage Source Headstage 1 •...
Page 65: Figure 3-8. I/O Control Panel
I/O Controls Figure 3-8. I/O Control Panel The ‘I/O’ tab contains the digital output and auxiliary analog output controls: Digital Output This section controls the holding bit pattern generated by the Digital Outputs of the amplifier. Sixteen TTL-compatible digital channels are displayed.
Page 66: Dynamic Clamp Editor
Auxiliary Output General purpose “auxiliary” analog output channels are available. These raw outputs can be used as holding levels, or for other external instrumentation. AuxOUT1 - 4 [ ±10,000 mV ] Select an auxiliary analog output channel and directly edit its voltage level, or use the spinners to change the value in 1 mV increments.
Page 67 Figure 3-9. Dynamic Clamp Editor [ Status Field ] Notifications on edits and file names are displayed here. Files and Pools [ drop-down list ] Most recently used list of the last 5 Conductance Pool file names. Load Conductance Load a previously saved Conductance Pool file Pool into the Conductance Pool.
Page 68 Revert to Last Saved Undo any unsaved changes to the Conductance Pool. Save Conductance Save the Conductance Pool using its existing Pool file name and path. Save Conductance Save the Conductance Pool to a new file, and Pool As switch to the new file. The default file name has an increment number appended to the original file name.
Page 69: Table 3-2. Conductance Pool
Load Load the selected Conductance and a check mark displays next to its name. Read-only notifications display. Save Pool Save the Conductance Pool using its existing file name. Add a default Conductance to the Conductance Pool, and open it for editing.
Page 70 Active Mode During Sweeps • Run Continuously • Update Rate [ 1, 2, 5, 10, 20, 50, 100, 200 kHz ] [ for Markov models, add: 250, 500 kHz ] Control the dPatch internal update rate of the conductance mod- eling during acquisition.
Page 71 SutterPatch as if it were the “cell’s” response to the dynamic- clamp stimulus current. AuxOUT3 [ for Headstage 1 tab ] • AuxOUT4 [ for Headstage 2 tab ] • Command Signal to AuxOut1 [ for Headstage 1 tab ] Enable extra output.
Page 72 Column 1]. This will call the external function “ReplaceQMatrix”, which allows you to manually calculate the Q Matrix. Contact Sutter Instrument technical support for additional details. Edit Model Parameters Windows Note: For Conductances with Channel Settings and Gate Settings, at least one chan- nel and one gate must be active.
Page 73 [ Channel 1, 2, 3 ] Active Enable the copying and execution of chan- nel settings. Label Enter a custom label for the channel, such as the ion species Channel 1: [ Na ] Channel 2: [ K ] Channel 3: [ Cl ] Copy Channel Copy channel parameters from an acti-...
Page 74 Gate 2: [ h ] Channel 2: Gate 1: [ n ] Channel 3: Gate 1: [ ] Copy Gate Copy gate parameters from an activated state. Exponent (1 – 4) Channel 1: Gate 1: [ 3 ] Gate 2: [ 1 ] Channel 2: Gate 1: [ 4 ] Channel 3: Gate 1: [ 1 ] Initial State...
Page 75 Channel 1: [ Na ] Channel 2: [ K ] Copy Channel Copy channel parameters from an acti- vated state. Pmax (cm/s) (0 – 100) Channel 1: [ 93 ] Channel 2: [ 0.0 ] Valence (±10.00 nS) Channel 1: [ 6 ] Channel 2: [ 1 ]...
Page 76 Initial State Channel 1: Gate 1: [ 0 ] Gate 2: [ 0 ] Channel 2: Gate 1: [ 0 ] α Alpha rate constant equation. Channel 1: Gate 1: [ 0.01*(V+35)/(1-exp((V+35)/-10)) ] Gate 2: [ 0.070*exp(-(V+60)/20) ] Channel 2: Gate 1: [ 0.010*(V+50)/(1-exp((V+50)/-10)) ] β...
Page 77 V_reversal Set to the reversal potential of the ion. (±200 mV) Channel 1: [ -72.140 mV ] Channel 2: [ 55.170 mV ] Number of States (2 – 14) Channel 1: [ 5 ] Channel 2: [ 8 ] State Equations (S0 –...
Page 78 [ 0.2*(V+35)/(1-exp((V+35)/-10)) ] [ (5, 6) ] [ 0.07*exp(-(V+60)/20) ] [ (6, 2) ] [ 8.0*exp((V+60)/-18) ] [ (6, 5) ] [ 0.1*(V+35)/(1-exp((V+35)/-10)) ] [ (6, 7) ] [ 0.07*exp(-(V+60)/20) ] [ (7, 3) ] S19 ] [ 12.0*exp((V+60)/-18) ] [ (7, 6) ] Edit State Matrix A modified State Matrix opens using state...
Page 79: Liquid Junction Potentials
Equation [ 0 ] [ 0 ] [ 1200 ] [ 0 ] [ 0 ] [ 0 ] [ 0 ] [ 0 ] Initial Probability Entries correspond to the number of states. All probabilities must add up to “1”. Initially starts at a closed state, but can be adjusted.
Page 80: Lock-In Adjustments
Online LJP Correction SutterPatch LJP correction is applied “online”, i.e., during acquisition, for automatic correction of whole-cell voltage levels. 1. Place an “open” micropipette into the bath in voltage-clamp mode. 2. Disable the Amplifier Control Panel offset ‘Lock’ control. 3. In the Amplifier Control Panel ‘Liquid junction’ field, enter your calculated bath-pipette solutions LJP value.
Page 81 Channel label. Computed membrane capacitance. Computed membrane conductance. Computed series conductance. DC component of measured signal. RealY Real number part of the lock-in response signal. ImagY Imaginary number part of the lock-in response signal. Cycles to Average [ 1 – 1000 ] Cycles to Skip [ 1 –...
Page 82: Using Peripheral Equipment
the results, and needs to be properly set - run the electrode compensation on a pulse, and then disable it, before running the LockIn adjustments. When tuning, start with the Phase Delay Adjustment, and then follow with the Attenu- ation Adjustment. The sensitivity of the SutterPatch software lock-in results is as good as for a hardware lock-in amplifier.
Page 83: Using Multiple Sutter Amplifiers
Note: The analog and digital controls in the Control Panel provide a way to quickly and easily test the behavior and operation of peripherals, without the need to create or modify Routines. 3.10.2 Using Multiple Sutter Amplifiers The dPatch amplifier is not supported for multiple-amplifier configurations. 3.10.3 Using Non-Sutter Amplifiers The dPatch system can also be operated as a stand-alone data acquisition system interfacing to non-Sutter amplifiers.
Page 84: Using Non-Sutter Data Acquisition Systems
3.10.4 Using Non-Sutter Data Acquisition Systems Due to the ultra-high bandwidth of the system, the dPatch system does not operate as a stand-alone amplifier or interface to non-Sutter data acquisition systems. 3.11 dPatch Maintenance This unit should require minimal maintenance when operated according to specifications. 3.11.1 Storage Pre-May 2021 dPatch systems store firmware-related information in volatile memory, which requires an internal battery for backup power.
Page 85: Figure 3-10. Calibration
Please contact Sutter Instrument Technical Support before you make any changes here! Figure 3-10. Calibration Copy to Clipboard Copy the calibration window to the system clipboard. DPATCH – OPERATION MANUAL – REV. 2.3 (2022-10-24)
Page 86: Table 3-3. Main Unit Calibration
Main Unit tab Gain Offset (mV) AuxOUT 1 – 4 0.500 – 1.500 ±5000 AuxIN 1 - 8 0.500 - 1.500 ±5000 Table 3-3. Main Unit Calibration Serial No Serial Number of the dPatch system. Part No Part Number of the dPatch system. Note [ Display of a text note.
Page 87: Current Clamp
Voltage Clamp Gain Offset (mV) Stim DAC 0.500 - 1.500 ±500.000 Current Clamp Gain Offset (mV) 200 nA Mode 0.500 - 1.500 ±5000.000 20 nA Mode 0.500 - 1.500 ±500.000 Table 3-4. Headstage Calibration Serial No Serial Number of the dPatch headstage. Headstage Part No Part Number of the dPatch headstage.
Page 88: Software Operation
4. SOFTWARE OPERATION 4.1 Acquisition SutterPatch acquisition operations. 4.1.1 Acquisition Control SutterPatch: Acquisition Control The interactive acquisition controls for Routines and Paradigms are grouped into this control panel. Figure 4-1. Acquisition Control Set Tag Click the Set Tag button to create a time-stamped text com- ment in the Paradigm metadata at any time.
Page 89 Note: Tag timing is not accurate in hardware emulation mode. Time [ hh:mm:ss ] The system time. [ only displays if enabled in Set Preferences / General / ‘Show time in Acquisition Control window’ ] Timer A running clock displays the time in “hh:mm:ss” since the last timer reset, or since a new experiment established a USB connection or emulation mode.
Page 90: Acquisition Measurements & Graphs
If measurement graphs are enabled, a docked “child” Analysis win- dow opens and plots sweep-by-sweep measurements. Stop Acquisition Terminate any running data acquisition. Stop at End of Sweep When ‘Stop at End of Sweep’ is enabled, and you click the ‘Stop Acquisition’...
Page 91: Acquisition: Routine Scope
4.1.3 Acquisition: Routine Scope The Acquisition: Routine Scope window is used for viewing and recording digitized time-series data, displayed as a smooth interpolated line. Figure 4-3. Acquisition: Routine Scope Window The Scope window is titled with the active Paradigm sequence number + Routine name. Note: Only one Scope window can be open at a time.
Page 92 Signals The central area of the Scope window graphically displays input data in up to 16 separate signal panes. Click on a signal pane to make it “active” - the Y-ais bor- der area displays in a lighter color, and the Y-axis controls (magnify, scroll) ap- ply to it.
Page 93: Figure 4-4. Axis Magnification
Axis Zoom  Figure 4-4. Axis Magnification When the mouse is moved into the X- or Y-axis area, the cursor changes to a double-headed arrow. As you click and drag the mouse cursor, a dark bar displays in the axis showing the magnification area; or, scroll the mouse wheel up/down to expand/shrink the X-axes or the active Y-axis.
Page 94 1. Move the mouse cursor into a signal pane - it changes into a large “+”. 2. Click and drag a bounding box around the desired data. (This box is also referred to as a “marquee”.) 3. Right-click in the marquee and select the desired action: Expand Applies to all signals.
Page 95: Figure 4-5. Axis Scroll Bars
Axis Scroll Bars  Figure 4-5. Axis Scroll Bars The X-axis scroll bar is directly underneath the X-axis, while the Y-axis scroll bar is on the far right-edge of the Scope window. Click and drag the scroll bar slider buttons, or use their directional buttons to move the dis- played signals in the desired direction.
Page 96: Figure 4-6. Center Button
Center  Figure 4-6. Center Button Center signal. Center the Y-range of the X-axis data in the active signal pane. The Y-axis offset is automatically adjusted, while the X-axis scaling is unchanged. To center all signals, shift-click the button. Y-Autoscale ...
Page 97: Figure 4-7. Autoscale Axes
Tip: To invert the Y-axis of the active signal, such as for data with reversed polarity from an outside-out patch, right-click in the Y- axis of the signal and select Axis Properties / Axis Range. Either reverse the Manual Range Settings / Minimum and Maximum values, or disable the Manual Range and enable the Autoscale Settings / Reverse axis.
Page 98 X-Scale  Autoscale all X-axes. Set the X-axis range to the maximum defined sweep duration for all signals. Persistence  Persistence data display. Enable: Overlay each new sweep of data onto the display of any prior sweeps. (per Scope Preferences limits). Disable: For each new sweep, all prior sweeps are cleared, and only the newest sweep is displayed.
Page 99: Figure 4-8. Signal Layout
Signal Layout  Figure 4-9. Signal Layout Signal pane layout. Set how the input signals are graphically arranged: Stack Vertical column of signals. • Single Only the active signal. • [ m x n ] Tiled array of signals in ‘m’ rows and ‘n’ columns. •...
Page 100: Figure 4-9. Amplitude Meters
Figure 4-10. Amplitude Meters For the Triggered Sweeps acquisition mode, each displayed signal has its own Y-axis amplitude meter on the inner right-side of its pane. For the Continuous Sweep acquisition mode, or if acquisition has not yet started, these meters are completely black. The height of the colored meter bars represents a signal’s data range vs.
Page 101: Other Buttons
warning sign to decrease your hardware gain. Red: Danger Signal too large. • (within 1% of, or at range limit) When an amplitude meter is dis- played in red, it indicates that the data might have gone out of range and be invalid.
Page 102 When acquisition is running, the Scope window updates every 200 ms. If the Sweep Start-to-Start time is ≥ 5 s, the “Time to next sweep: # s” is reported below the Start / Stop buttons. If Metadata prompts are configured for Routines or Paradigms, the Con- firm Metadata Settings dialog displays just before recording begins.
Page 103: Table 4-1. Other Scope Buttons
Analyze with Saved Default Measurements Save as Default Measurements Edit Measurements: Open a special Reanalysis Measurements & Graphs dialog where all changes apply instantly to the measurements and the graphs, even during acquisition. These edits override the loaded routine for quick interactive control. ______________________________________________________________ Parametric Plot Plot the relationship between two signals.
Page 104 Scope Settings Set all marks in sweeps of active series by equation Opens the ‘Sweep Mark: Equation Editor’ to enter an equation for the sweeps to mark. Equation Undo Remove all edits to the equation. Check Equation Check the equation syntax. The equation is evaluated, and if valid, it reports "Syntax is ok.”...
Page 105 Full Trace Use the entire trace for the time range. Sweep Time Set relative to the start time of a sweep (time zero). Start Time Set the starting time. Once the Start Time is within 2 ms of the End Time, further Start Time increments will increase the End Time by the same amount.
Page 106 Sweep Time Set relative to the start time of a sweep (time zero). Start Time Set the starting time. End Time Set the ending time. Segment Time Set the time range as a ratio relative to the Segment duration. Segment Select the Segment number.
Page 107 Signal List of available signals. The color graph is based on the selected input sig- nal name. If no such signal name exists in the current Series, the color graph is blank. [ range ] Select the Y-range to be used for a Plot. Auto Y Range Use an autoscaled Y-axis range for the data.
Page 108 Autoscale X Axis Set the X-axis for all signals to the maximum de- fined sweep duration. Set X Scale… Manually set the X-axis range. X-min The minimum X-axis value. X-max The maximum X-axis value. Axis Properties… Modify the axes style and components. Y Axis Autoscale All Axes Scale all signals Y-axes to their existing data, and...
Page 109: Main Window
Or, if Y-axis autoscaling will be used: Click the ‘Uncheck Both’ button, and… Autoscale Settings Autoscale Only Visible Data: Disable. Reverse axis: Enable. Hide Signal <name> Hide the selected signal in the Scope window. Show Signal <name> Only Show the selected signal in the Scope window, hide all other signals.
Page 110 graph background The background of the pane. all axes The X- and Y-axis areas. all grids The grid lines in the pane. all tick labels The tick labels in the X- and Y-axis areas. all axis labels The axis labels in the X- and Y-axis areas. Hide Signal ‘<name>’...
Page 111: Signal Data
Horiz Shrink Move all signals X-axes current limits to the posi- tion of the marquee horizontal data limits. Vert Shrink Move the signal’s Y-axis current limits to the posi- tion of the marquee vertical data limits. Extract Template Copy the last sweep to the Template Editor. Extract To Graph Display the first trace in a floating window, using all data within the X-range.
Page 112 Cursor A Cursor symbol for data point ‘A’. Symbol letter (beginning cursor of the pair). R1_A_IV (Default) wave name. Draggable cursor mover tool for the cursor pair. pnt: Data point number (starting from zero). X-axis value of data point ‘A’. Y-axis value of data point ‘A’.
Page 113: Camera Control
field. X- and Y-measurements are displayed for the cursor pair data points. 5. Fitting can also be applied to the cursor pair data. Right-click on the data, and select ‘Quick Fit’ for a list of built-in Igor Pro fitting functions. The fit is displayed in the graph, and the fitting information is written to the Command window.
Page 114 Capture Take a single picture. If live video is running, this will take a picture while live video continues to run. The image time-stamp is reported in the Log window. Last Capture A thumbnail of the last picture taken in the Experiment is displayed. All pictures are stored in the current Experiment.
Page 115: Free Run
4.1.5 Free Run SutterPatch: Free Run (Scope) The Acquisition: Free Run Scope window simulates a one- or two-channel oscilloscope, and is a quick method of viewing repetitive data. Figure 4-12. Free Run Scope DPATCH – OPERATION MANUAL – REV. 2.3 (2022-10-24)
Page 116 This window operates similarly to the Acquisition: Routine Scope window, with unsupported controls removed or disabled. However, when this Scope window is initially created, the Autoscale button is set to the last used state, instead of using a Preferences setting. Additional controls were also added: The ‘storing data to disk’...
Page 117 Active Headstage Headstage1 Headstage2 AuxIN1 - 8 Bandwidth [ Headstage channels ] [ I-Filter, V-Filter ] Set by the Amplifier Control Panel filter. This low-pass filter is applied to a headstage input signal sampling rate. During acquisition, filter controls are locked, as they affect the sampling rate.
Page 118 occurs. Warning! Processing very large data sets can overload system resources. Integrator Reset [ Headstage: Capacitive Mode] When using the amplifier’s Capacitive mode, choose how to handle undesirable data transients generated by capacitor discharges (resets). Ignore Capacitive mode reset transients are displayed in the data (unless the Control Panel ‘Settings’...
Page 119 input signal sampling rate. During acquisition, filter controls are locked, as they affect the sampling rate. Note: Filtering is not applied in Demo mode. Demo data is acquired with a “Nyquist Factor-adjusted” sampling rate. Sampling Rate [ Auxiliary channels ] [ 1, 2, 5, 10, 20, 50, 100, 200 kHz ] Set the auxiliary input channel sampling rate.
Page 120: Membrane Test
Ignore Capacitive mode reset transients are displayed in the data (unless the Control Panel ‘Settings’ is ena- bled for ‘Subtract capacitor reset transients’. Blank The data during capacitive transients are made invisible by replacing those data points with NaNs (Not a Number). Mask The data during capacitive transients are replaced by the last...
Page 121: Figure 4-12. Membrane Test Scope
Figure 4-13. Membrane Test Scope Acquisition: Membrane Test This scope window operates similarly to the Acquisition: Routine scope window. By default, this scope window’s top pane displays the Current signal from the active Sutter headstage, and the pane beneath it displays the corresponding Voltage command signal. Differences to the scope window for the Membrane Test: Unsupported buttons were removed: Persistence Display, Signal Layout.
Page 122 The Sweeps Counter only displays when the Membrane Test is run from a Para- • digm with numbered “Repeats” configured. The first time the Membrane Test is opened, it is in a “stopped” state to allow • setup and configuration. Thereafter, re-opening the Membrane Test automati- cally uses the last acquisition status of its scope window.
Page 123: Figure 4-13. Membrane Test Settings
Membrane Test Settings Configure all Membrane Test parameters in the Membrane Test Settings panel. Figure 4-14. Membrane Test Settings Show Monitor Only • Monitor + Test Pulse • All Settings • DPATCH – OPERATION MANUAL – REV. 2.3 (2022-10-24)
Page 124 Open the Membrane Test ‘Preferences’ settings dialog. Membrane Test Preferences Second Membrane Test channel Display the controls for a second input channel in the Sig- nal Parameters section. MT analysis on second channel Display the controls for a second analysis channel in the Measure Parameters section.
Page 125 Averaged Traces Set display options for the last “N” traces used in the run- ning average trace. These only display when the Measure Parameters ‘Display’ is set to ‘All’. Line Thickness [ 0.25, 0.50, 0.75, 1 – 10 ] Color Open a color selection panel.
Page 126 Seal Rseal (MΩ) Seal Resistance meter. [ Model cell = ~1 GΩ to 1 TΩ ] (open circuit) Cell Rseries (MΩ) Series Resistance meter. [ Model cell = ~10 MΩ ] Rmembrane (MΩ) Membrane Resistance meter. [ Model cell = ~500 MΩ ] Cmembrane (pF) Membrane Capacitance meter.
Page 127 RSeries = 10 MOhm Cell Compensation Rs CFast = 5 pF Electrode Compensation CFastTau = 4 µs Electrode Compensation PipResistance = 10 MOhm Rpipette SealResistance = 1 GOhm Rseal CellResistance = 500 MOhm Rmembrane Write To Log Click the ‘Write To Log’ button to write the last acquired measurements for that mode to the Log window.
Page 128 frequencies up to 2 kHz,. At higher lock- in frequencies, we recommend disabling the whole-cell capacitance compensation, else the lock-in phase delay is affected and requires manual adjustment. Lock-in 2.0 ms (500 Hz) • Lock-in 1.0 ms (1 kHz) • Lock-in 0.5 ms (2 kHz) •...
Page 129 Zap Parameters (This feature is only active in voltage-clamp mode.) After a gigaohm patch has been achieved, use Zap in the Seal mode to disrupt the cell membrane, as an alternative to suction in creating a whole-cell patch. Amplitude Set the amplitude of the square wave zap pulse. [ ±750.00 mV ] Duration [ 0.040 –...
Page 130 Display Stimulus Add a channel to the Scope window for the stimulus signal. Second Channel The “Second Channel” is optionally enabled in the Membrane Test Settings ‘Preferences’ menu. No Channel Inactive Headstage The headstage that is not selected • or highlighted. Headstage1 - 2 •...
Page 131: Paradigm Editor
Measurements are derived from the last trace average (except for Lock-in and Noise measurements). The averaged trace displays in red. The average is reset when the main mode is changed (Bath – Seal - Cell). Display Scope window signal display options. Signal The active signal data trace is displayed.
Page 132: Figure 4-14. Paradigm Editor
running Routines and directly controlling amplifier settings. Figure 4-15. Paradigm Editor Loaded Paradigms display on the left, while loaded Paradigm Steps display on the right. A bottom section can display interactive checkbox controls and/or variables. Controls Start/Stop Paradigm, Set Tag and Reset Timer controls are located in the Acquisition Control panel.
Page 133 step execution. This display is dependent upon Show Editor Controls. Show/Hide Variables: A Variables table can be displayed at the bottom of the Paradigm Editor. These paradigm variables can be utilized in any equation. Variable names can be edited to any label, but they are only informational, and are not supported in equations.
Page 134 Send Last Used List to Command Copy the pathname of the ‘Files and Pools’ last used Para- digm Pool to the Command window history. Clear Last Used List Clear the “Last Used” Pool list of all entries. File path of the loaded Paradigm Pool file. Paradigm description: A user description of the active Paradigm.
Page 135 appended to the name. Duplicate Add a copy of the selected Paradigm to the Paradigm Pool. The Paradigm name number is appended or incremented. Delete Remove the selected paradigm from the Paradigm Pool. Revert Select a paradigm and click the ‘Revert’ button. All editable steps are reset to their originally loaded values, as long as the Paradigm Pool has not been saved.
Page 136 Reset Timer Scope Operation Set Axis Set Checkbox Set Mark Set Metadata Set Solution Set Tag Set Variable Set Write Steps Sound Start New Paradigm Data Update Inputs View Last Write to Log Write to Notebook ----- Alert Beep Comment Pause Wait Wait for Trigger...
Page 137 Break Chain For Loop Jump Label ------------ Condition ElseIf Else (See details in Insertable Steps list below.) Edit If a highlighted Step is configurable, clicking the Edit button (or double-clicking the step) will open it in the Paradigm Steps Editor for configuration. Also, if a highlighted Step’s text is partially hidden, use the Edit button to view the entire entry.
Page 138 Revert Select a Step to be reverted, and click the Revert button. Editable fields are reset to their originally loaded values, as long as another Paradigm has not been loaded. Delete Delete the selected step. For multi-line steps, optionally delete the step without deleting the contents of the step.
Page 139: Amplifier
Set Checkbox Set Solution Set Variable Wait Write All Write All Steps • Log the main steps and additional steps into the Paradigm metadata (visible in the Metadata ‘By Event’ view.) Insertable Steps Amplifier Control the dPatch amplifier hardware. Figure 4-16. Paradigm Step: Amplifier Default Setting: Amplifier, Target=VHold, Equation=-0.080 Close the ‘Paradigm Steps Editor’.
Page 140 For a single headstage system, the active probe is always headstage number "1". dPatch Settings CCMode (amplifier current clamp) Place the amplifier into Current-Clamp mode. VCMode (amplifier voltage clamp) Place the amplifier into Voltage-Clamp mode. Hold (IHold in CC-mode, VHold in VC-mode) [ ±0.000,000,020 A (±20 nA), or ±1.000 V ] Set the active headstage holding level.
Page 141 IGain (amplifier current gain, V/A) Set the gain for the active ‘Current’ input channel using standard unit numbers (V/A) or scientific notation (1 mV/pA = “1e9”). The value is converted to a preset Gain level: mV/pA • mV/pA • mV/pA •...
Page 142 ±20 nA range • ±200 nA range • Filter (amplifier input filter in VC- and CC- mode, Hz) Set the filter level of the active input channel: (500 Hz) • 1000 (1 kHz) • 2000 (2 kHz) • 5000 (5 kHz) •...
Page 143 5000 (5 kHz) • 10000 (10 kHz) • 20000 (20 kHz) • To help prevent over-filtering, exceeding a 10% threshold between levels promotes the equation value to the next higher filter level. Offset (amplifier pipette offset in VC-mode, V) [ ±0.5 ] Adjust the active output channel to remove any hardware- and/or solution- related offsets.
Page 144 Set a cell capacitance value and enable cell capacitance compensation. RsComp (amplifier cell compensation Rs, Ohm) Set a series resistance value and enable cell capacitance compensation. RsCompOn (amplifier cell compensation On) [ 0 = Off , 1 = On ] Bridge (amplifier bridge balance, Ohm) BridgeOn...
Page 145 AutoBridgeAmpl (amplifier auto bridge compensation amplitude, A) Reset (reset amplifier controls) ResetCap (reset capacitor in capacitive feedback mode) Avoid capacitor reset transients in data recordings by generating a reset before each sweep; use the Paradigm ‘Each Sweep’ step with the Amplifier step option ‘ResetCap’...
Page 146 DynHoldAqOn (amplifier dynamic active while acquiring) Auxiliary Output AuxOUT1 (Auxiliary Output-1, V) AuxOUT2 (Auxiliary Output-2, V) AuxOUT3 (Auxiliary Output-3, V) AuxOUT4 (Auxiliary Output-4, V) Digital Output DigOUTWord (Digital Output Word) DigOUT1 - 16 (Digital Output-1 - 16) Lock-In LockInAdjustOn (set LockIn adjustments On) LockInPhaseAdj (set LockIn phase delay adjustment) LockInAttenAdj...
Page 147: Each Sweep
list below.) Each Sweep Control the Paradigm operations on a “per sweep” basis of a Routine. Commands to be executed are inserted between the “EachSweep, Target” line and the “ForEachEnd” line. Figure 4-17. Paradigm Step: Each Sweep Default Setting: ForEachSweep EachSweep, Target=untitled ForEachEnd Close the ‘Paradigm Steps Editor’.
Page 148 Undo Remove any unsaved edits to this step. [ drop-down list ] Select an Acquisition type, or a Routine to record a data Series. The time from starting this command to recording data is +300 ms. Membrane Test • Repeats [ 1 –...
Page 149: Analysis
Add Channel [ Clear ] Clear the selected channels list. [ Headstage1 – 2, AuxIN1 – 8 ] Available input channels. [ selected channels ] List of Routine names from the loaded Routine Pool. • [ selected Routines ] Edit routine “<name>” Open the selected Routine for editing in the Routine Editor.
Page 150: Camera
[ Operations ] Save to Editor Save the latest analysis. • Append to Last Append to the prior analysis. • Average with Last Average with the prior analysis. • Concatenate Concatenate with the prior analysis. • ------------ Show Table Display the analyses as a numeric table. •...
Page 151: Clear Key
Clear Key Clear the ‘Last key’ field in the Paradigm Editor, which holds the last-pressed keyboard key since the start of the Paradigm. Default Setting: ClearKey Dynamic Clamp Load a Dynamic Clamp model from the active Conductance Pool. Figure 4-21. Paradigm Step: Dynamic Clamp Default Setting: DynamicClamp, Model= Close the ‘Paradigm Steps Editor’.
Page 152 Command window, including user-created Functions. Note: Igor Pro syntax usually requires that open/close parentheses “( )” be appended to the end of a command, however exceptions include the “beep” and “print” commands, for which no parentheses are used. Insert Special Identifier Special references can also be used within commands: s[series-count, sweep-count, trace-count,...
Page 153 Ex: s[0,0,0,] The Acquisition: Routine Scope window active Series, active sweep, and active trace of the active Routine. t[#] (trace of current sweep of • current series) Reference the input trace in the open Scope window channel position “#”, for the active sweep of the active Series of the active Routine.
Page 154: Export
FFT t[2] If, Left=sweep, Operation=”=”, Right=1 Execute, Command=Display Volt- age1_FFT EndIf Execute, Command=SetAxis Bottom 0,60 ResetTimer 9. ForEachEnd In Step 2: Replace “YourRoutineName” with your own Routine name, or use the sample “IV” Routine. In Step 3: The Igor Pro ‘FFT’ command is run, and “t[2]”...
Page 155: Front Window
Graphs stacked. 2 x 2 Matrix display. 2 x 4 Matrix display. [ Add Signal list ] Select signals to be exported from a list of default names. Clear Clear the signal field, set it to ‘off’’. Select all entries. All Signals Select all input signals.
Page 156: Hide Window
Camera Window Control Panel Dashboard Data Navigator Equation Editor Log Window Paradigm Editor Routine Editor Scope Window Shortcut Editor Solution Editor Template Editor Hide Window Hide the specified window. Figure 4-25. Paradigm Step: Hide Window Default Setting: HideWindow,Target=Scope Window Close the ‘Paradigm Steps Editor’. Undo Remove any unsaved edits to this step.
Page 157: Reset Timer
Shortcut Editor Solution Editor Template Editor Reset Timer Reset the Paradigm Editor Timer to 00:00:00. Default Setting: ResetTimer Scope Operation Control which Scope window signals are displayed, and how the sweep display operates. Figure 4-26. Paradigm Step: Scope Operation Default Setting: Scope, Wipe=false Close the ‘Paradigm Steps Editor’.
Page 158: Set Axis
• • Autoscale A one-time autoscale of the Y-axes of all selected signals to their incoming data, i.e., to their visible sweeps data limits, and resets the X-axes to the full sweep duration. Center Center the active signal so the mean of the Y-axis data is vertically centered in the signal pane.
Page 159: Set Checkbox
[ drop-down list ] Select the axes orientation. Left Set the Y-axes on the signal list. • Bottom Set the X-axes of all signals. • [ drop-down list ] [ Bottom ] Select the X-axis scaling to apply. Full scale Display the full range of the axis.
Page 160: Set Mark
Figure 4-28. Paradigm Step: Checkbox Default Setting: Checkbox, Count=1, Equation=true Close the ‘Paradigm Steps Editor’. Undo Remove any unsaved edits to this step. Checkbox Checkboxes [ 1 – 3 ] are local: they are cleared whenever a Paradigm is started. Checkboxes [ 4 –...
Page 161 Figure 4-29. Paradigm Step: Set Mark Default Setting: SetMark, Value=Set Close the ‘Paradigm Steps Editor’. Undo Remove any unsaved edits to this step. Mark • • Clear Toggle • “Marking unmarking” a sweep marks/unmarks that sweep in all signals in the same Series. Marked sweeps are loaded into the Data Navigator as “marked”.
Page 162: Set Metadata
Set Metadata Define Metadata parameter values to apply to the data during acquisition. The ‘Set Metadata Paradigm Step Value’ dialog opens for configuration: Figure 4-30. Paradigm Step: Select Metadata Group Default Setting: Metadata, Value= Select Metadata Group To change the metadata detail level, go to Preferences > Metadata. DPATCH –...
Page 163 Operator [ Full detail level ] • Preparation – Animal [ Basic detail level ] • Preparation – Tissue [ Basic detail level ] • Preparation – Cell [ Basic detail level ] • Experiment [ Basic detail level ] •...
Page 164: Set Solution
Set Solution A “solution” command is used to turn solution valves ‘on’ or ‘off’ in perfusion systems. A predefined digital pattern or analog level can be automatically output with this step. Solution settings are configured and numbered in the Solution Editor. Figure 4-31.
Page 165: Set Variable
Note: The comment text for this Paradigm step is maintained separately from the manually triggered Acquisition Control ‘Set Tag’ button text. Set Variable Variables allow flexible control of any operation that uses equations. Figure 4-33. Paradigm Step: Set Variable Default Setting: SetVariable, Target=Paradigm, Count=1, Equation=p[1] Close the ‘Paradigm Steps Editor’.
Page 166: Set Write Steps
< Routine Names > • Select a Routine and set the value of its Variable_r[#] [ 1 – 16, All Variables ] When ’All Variables’ is selected, if varying values are desired, enter their values into the Equation field as a comma-separated list; simple equations (those without internal commas) can also be used in place of a value.) If there are more variables than list values, the...
Page 167 [ Drop-down list ] Write No Steps • Write Main Steps • Action-oriented steps are recorded in the Paradigm metadata (visible in the Metadata ‘By Event’ view): Amplifier Break Camera Chain Execute For Each Sweep Reset Timer Routine Set Checkbox Set Solution Set Variable Wait...
Page 168: Sound
Sound Output a note from the computer speaker. The frequency can be defined by a fixed value or an equation. Figure 4-35. Paradigm Step: Sound Default Setting: Sound, Equation=, Volume=1 Close the ‘Paradigm Steps Editor’. Undo Remove any unsaved edits to this step. Equation (Hz) [ 250 –...
Page 169: Start New Paradigm Data
Output is via the standard sound output that Igor Pro uses: Windows: Built-in speakers, or a computer sound card • with external speakers. Note: Lower frequency tones are attenuated in volume on lower-quality speakers. macOS: Built-in speakers • This paradigm step can also be utilized as an Igor Pro programming command.
Page 170: Write To Log
Write to Log Enter text to be written to the Log window. Figure 4-36. Step: Write to Log Default Setting: WriteLog, Alert=true, Text=text_to_write, Equation=, DoBeep Close the ‘Paradigm Steps Editor’. Undo Remove any unsaved edits to this step. Do Beep Generate a beep before writing.
Page 171: Write To Notebook
Paradigm: Write to log This run-time dialog displays when the Paradigm step is executed: Figure 4-37. Step: Write to Log Run-Time Window Elapsed time A time counter for the Alert. Text Edit the text message. Continue and Write Write to the metadata. Continue, no Write Do not write to the metadata.
Page 172: Alert
Format [ Time, Date, 3 – 12 digits ] For the ‘Time’ format, seconds are converted into Hours:Minutes:Seconds.Milliseconds. For the ‘Date’ format, seconds are converted into Year-Month-Day as XXXX-XX-XX. The starting date is “1904-01-01”. No rounding is done. For numbers, set the number of significant digits to display in scientific exponential notation.
Page 173: Beep
Beep Generate a “beep” sound from the computer speaker. Default Setting: Beep Comment A text message can be displayed in a floating window. Figure 4-40. Step: Comment Default Setting: Comment, Text= Close the ‘Paradigm Steps Editor’. Undo Remove any unsaved edits to this step. Comment Enter the comment text.
Page 174: Wait
Wait Temporarily pause execution of the Paradigm for a defined duration. Figure 4-41. Step: Wait Default Setting: Wait, Source=.Time=1 Close the ‘Paradigm Steps Editor’. Undo Remove any unsaved edits to this step. [ Given value, Variable p[1] – p[16] ] Seconds to Wait [ displays for “Given value”...
Page 175: Flow Control: Break
Click the spinners for 0.001 V increments, or type in a value. Edge [ Rising, Falling ] Flow Control: Break Use a Break step to stop the execution of a Paradigm, or to interrupt For Loop and For Each Sweep loops. Figure 4-43.
Page 176: Flow Control: For Loop
Paradigm to chain to: Paradigm execution will shift to the selected Paradigm. For multiple Chains (or recursive calls), you can link a maximum of eight Paradigms. Edit paradigm “<selected Paradigm>“ Load the selected Paradigm for editing. Flow Control: For Loop Use a standard programming “For loop”...
Page 177: Flow Control: Label
Close the ‘Paradigm Steps Editor’. Undo Remove any unsaved edits to this step. Jump Target Enter the Label of the step to jump to. Flow Control: Label Create a target step Label for a Jump step, to change the sequence of execution.
Page 178 Undo Remove any unsaved edits to this step. [ drop-down list ] Operation selection. Compare 2 equations • Left Equation Evaluated to a value. Check Equation Check the equation syntax. The equation is evaluated for sweep #1, and if valid, it reports "Syntax is ok.”...
Page 179 the start of a Paradigm. Key to check for Enter a text key, or insert a “special” key. Insert special key Use a “non-text” key. Space • Return • • Check checkbox status Select a checkbox to monitor for • “on / off”...
Page 180: Condition: Elseif
Condition: ElseIf Allow conditional Paradigm flow control between multiple choices. Figure 4-49. Step: Else If Default Setting: ElseIf, Left=, Operation=’>’, Right= Close the ‘Paradigm Steps Editor’. Undo Remove any unsaved edits to this step. [ drop-down list ] Operation selection. Compare 2 equations •...
Page 181 comparing two floating- point numbers for equality, as minor variations in resolution can affect the outcome. Right Equation Evaluated to a value. Check Equation Check the equation syntax. The equation is evaluated for sweep #1, and if valid, it reports "Syntax is ok.”...
Page 182: Condition: Else
Do Beep Your computer beeps once when the alert displays. Alert Text [ Enter your alert question text. Run-time dialog Elapsed Time A timer of how long the Alert has been displayed. ‘Yes' button (value = 1) ‘No’ button (value = 0) Stop Paradigm Manually abort the Paradigm.
Page 183 Figure 4-51. Paradigm Variables These variable can be used in any equation, or in the Paradigm step Execute, and persist across experiments. The table can be directly edited during non-acquisition, or set via the Paradigm step Set Variable. ‘Close’ button Closes the Variables table.
Page 184 Sweep (active paradigm EachSweep count) Sweep count of the active sweep in the Scope window. LastSweep (active paradigm sweep countof last sweep) During acquisition, this is set according to the Routine parameters. Once acquisition terminates, this is replaced by the count of the last acquired sweep, i.e., the last sweep in the stored Series.
Page 185 m[1..16] (n’th analysis measurement value) gx[1..16] (n’th analysis graph x value) The X-value of the last data point in the latest version of graph[#]. gy[1..16] (n’th analysis graph y value) The Y-value of the last data point in the latest version of graph[#].
Page 186 the system. dPatch Settings CCMode (amplifier current clamp) [ 0 = Off, 1 = On] VCMode (amplifier voltage clamp) [ 0 = Off, 1 = On] Hold (IHold in CC-mode, VHold in VC-mode) [ ±0.000,020 A (±20 nA), or ±1.000 V ] Headstage holding level.
Page 187 ±87200 nA range • Filter (amplifier input filter in VC- and CC-mode, Hz) Read the low-pass filter of the active input channel. IFilter (amplifier input filter in VC-mode, Hz) Read the low-pass filter of the ‘Current’ input channels. VFilter (amplifier input filter in CC-mode, Hz) Read the low-pass filter of the ‘Voltage’...
Page 188 ECompTau (amplifier electrode compensation tau, s) ECompOn (amplifier electrode compensation On in CC- mode) [ 0 = Off, 1 = On] CmComp (amplifier cell compensation Cm, F) RsComp (amplifier cell compensation Rs, Ohm) RsCompOn (amplifier cell compensation Rs On) [ 0 = Off, 1 = On] Bridge (amplifier bridge balance, Ohm) BridgeFraction...
Page 189 DynCGHold2 (amplifier dynamic Clamp G-holding 2, S) Dynamic Holding DynHoldOn (amplifier dynamic holding On) DynHold (amplifier dynamic holding potential, V) DynHoldSpeed (amplifier dynamic holding speed) DynHoldAqOn (amplifier dynamic holding active while acquiring) Membrane Test Relectr[1..2] (electrode/seal/access resistance, Ohm) Value from last Membrane Test. Rmemb[1..2] (membrane resistance (cell mode), Ohm) Value from last Membrane Test.
Page 190: Routine Editor
4.1.8 Routine Editor SutterPatch: Routine Editor Routines contain the settings that are in effect during data acquisition. The Routine Editor allows you to define acquisition parameters, set input and output channels, and to create stimulus waveforms and online analyses. The Routine Editor is the central place to create and manage saved Routine Pools and data acquisition settings.
Page 191 Show Action Setting Controls Enable the display of “in-sweep” Actions. Apply control panel changes based on time or amplitude triggers. Routine Settings Set Membrane Test Segment Amplitude. Status field: Notifications on edits and Routine names are displayed here. [ drop-down list …] Files and Pools List of the 5 most recently used Routine Pool files.
Page 192: Table 4-2. Routine Files And Pools
Pool. Re-assign the analog input and output channels in a ‘Mappings’ dialog that opens. [ The amplifier hardware must be attached to enable this option. ] Convert Routine Pool Convert the loaded Routines (designed for other in- struments) to be compatible with the attached am- plifier or emulation mode.
Page 193 the loaded pool to populate the new pool. Pathname of the loaded Routine Pool file. Routine Description A text comment can be edited and saved with the Routine. Store data during Routine execution. This button is green when enabled, and red when disabled. Routine Pool The Routine Pool section lists the names of all currently loaded Routines.
Page 194: Table 4-3. Routine Editor Buttons
Activate Open or refresh the Acquisition: Routine Scope window with the lat- est Routine settings, but do not start acquisition. This button is re-named to “In Progress” during a recording. Execute Open or refresh the Acquisition Scope window and immediately start recording.
Page 195 Waveform Preview The stimulus waveform is graphically displayed at the bottom of the Routine Editor. Figure 4-54. Waveform Preview Pane The waveform preview and its settings are updated live to reflect changes in the Waveform Editor and Amplifier Control Panel. Measurement regions can be manually repositioned in the Preview pane.
Page 196 In the preview pane, click and drag the mouse cursor to surround a region of interest • with a bounding box (the “marquee”). Right-click in the box and select one of the expand/shrink options. Some key settings and display controls are listed on the right of the Preview pane. Units are in ‘s’, or if <...
Page 197 All Dig Bits Preview all digital output bits. • [ list ] Select from the enabled output channels. • Show Trace: Select how to display autoscaled sweep traces in the preview pane: Time Course Display all traces in continuous linear •...
Page 198: Acquisition & Routine Parameters
Acquisition & Routine Parameters Acquisition timing parameters are controlled in this section, such as sweep duration and sam- pling rates. The settings in this section are shared by all input and output channels. Figure 4-56. Acquisition & Routine Parameters Trigger Action Control how and when recordings occur.
Page 199 Once a sweep has been triggered, additional triggers are locked out until the sweep has been completed. The refractory period, i.e., the time during which another event trigger cannot occur, is the same as the ‘Sweep Start-to-Start Time’. Note: If this option is grayed out, first set the Trigger Action to ‘Clock Triggered’...
Page 200 before the event trigger. Trigger Threshold [ ±20.000 nA ] current input [ ±0.75 V ] voltage input Trigger Polarity Rising Falling Minimum Trigger Duration [ 100 µs – 56.00 ms ] Acquisition Mode Triggered Sweeps: Each sweep is started by an internal software trigger •...
Page 201 Also, the amplifier VC/CC mode is set here, as the Output Channels section is una- vailable when outputs are disabled. Restrict To Ensures that the matching headstage is in the proper VC/CC mode, else the Routine cannot be activated or executed. VC Mode The Amplifier Control Panel matching headstage must be in •...
Page 202 Sweep Start-to-Start Time [ ‘s’ or ‘ms’ ] The time from the start of recording a sweep to the start of the next sweep recording. For Externally Triggered and Event Triggered acquisition modes, this serves as a “refractory period”, during which time additional triggers are not accepted.
Page 203: Input Channels
Input Channels Configure the input channels. Each channel has its own settings. Figure 4-57. Input Channels Edit Signal [ for disabled Output Waveforms ] When Output Waveforms are disabled in the Acquisition Parameters section, Segment timing can still be controlled via a modified Waveform Editor. This signal editor is a “...
Page 204 When this button is enabled, double-clicking a channel will open the signal Waveform Editor. Channel Enable up to sixteen Input Channels for recording data: Current# Analog input current channels hardwired from the dPatch headstage. At least one “Current” channel needs to be enabled when recording in Voltage Clamp mode.
Page 205 enter the new name. If the label is used by another channel, an underscore and increment number are appended to the new label. When a Virtual input channel is enabled, a default ‘Math Type’ label is automatically generated for it. Unit The base unit of measurement.
Page 206 channel. Recording Mode [ only editable for Auxiliary input channels ] Displays the patch-clamp recording mode assigned at the start of acquisition. VC_Mode Voltage-Clamp mode • CC_Mode Current-Clamp mode • ------------------- Scope Position The input channel panes can be repositioned in the Scope window. Position “1”...
Page 207: Digital Out
Input Bandwidth Total Filter Delay 1000 kHz 16.2 µs 500 kHz 17.0 µs 250 kHz 18.5 µs 10 kHz 85.0 µs Note: In Demo mode, demo data uses the Nyquist Factor sampling rate timing instead of the Filter Bandwidth timing. In Sweep Action [ for headstage input channels ] [ only displays if Routine Settings...
Page 208 Recording Mode Configure fast ( µs vs. ms) automatic headstage “VC | CC” mode switching during acquisition. Action Trigger Fixed Position Set a “sweep time” to switch the • recording mode. Switch At [ 0.00 s – sweep duration ] Threshold [ OFF ] Threshold Polarity...
Page 209 Threshold Polarity [ OFF ] Relative to Threhsold Set an input trigger level to • change the Holding level. Delay from Threshold [ 0.00 – sweep duration ] Threshold [ ±20.0 nA, ±1.000 V ] Threshold Polarity Rising Edge • Trailing Edge •...
Page 210 Rising Edge • Trailing Edge • Dynamic Holding [ OFF, ON, keep ] Target Voltage [ ±750 mV ] [ 10 ms – 60 s ] Revert Action Do not switch back to the original Dynamic Holding level. Switch back to the original Dynamic Holding level.
Page 211 Digital State [ Digital Word: 0 – 65.5 k, DigOUT#: 0, 1 ] Revert Action Do not switch back to the original digital output state. Switch back to the original digital output state. Revert At [ ms ] Delta time after the trigger. AuxOut Configure automatic auxiliary output channel level changes during acquisition.
Page 212 Switch back to the original auxiliary output level. Revert At [ ms ] Delta time after the trigger. Oscillation Catcher Protect against excessive noise or oscillation. Max Deviation [ 0 – 100% ] • Max RMS [ 0 – 100% ] •...
Page 213 VC mode: ‘Current#’ signals • CC mode: ‘Voltage#’ signals • Select the filter bandwidth of the channel. [ Use Control Panel ] Set the ‘Current’ and/or ‘Voltage’ channel bandwidths via the Amplifier Control Panel. [ 100, 200, 500 Hz; 1, 2, 5, 10, 20, 50 kHz; 100, 250, 500, 1000 kHz (enable in dPatch settings) ] Warning! Processing very large data sets (i.e., using very high filter...
Page 214 When a filter bandwidth is selected in the Routine, it replaces the Amplifier Control Panel I-Filter or V-Filter setting while the Routine is acquiring Series data. However, when acquisition stops, the Control Panel filter normally returns to its original setting. Enable this option to retain the Routine filter value in the Amplifier Control Panel after acquisition stops.
Page 215 Calculated by applying the Nyquist factor to the filter bandwidth. Integrator Reset [ only displays if ‘Capacitive Mode’ is set in the Amplifier Control Panel ] [ for headstage “response” input signals ] VC mode: ‘Current#’ signals • CC mode: ‘Voltage#’...
Page 216 LineFreq LockIn Smooth Stimulus SweepAverage SweepSubtract BaselineSubtract • Subtract a fixed value from all data points in an input trace. This is useful for adjusting an offset or resetting a baseline. Post-analysis is limited to marked sweeps if the Reanalysis Scope Measurements button / Edit Virtual Signals.
Page 217 End Ratio Set the ending time of the data to be averaged, as a ratio relative to the ending time of the Segment duration. End Time [ derived value ] BesselFilter A frequency-domain filter with excellent response • characteristics for preserving the shape of a biological signal. Source Channel Select an input channel to filter.
Page 218 Mask The data during capacitive transients • are replaced by the last data value before the transient discharge, simulating a sample-and-hold operation. Blank/Mask Duration [ 50.00 µs – 1.00 s ] The default value of 500 µs should be sufficient to encompass the reset transient duration.
Page 219 as a tool tip, by hovering the mouse cursor over the ‘Math Equation’ field. Specify math equation for virtual signal [ <equation> ] A free-form text field. Errors are reported under this field. Check Equation Check the equation syntax. The equation is evaluated for sweep #1, and if valid, it reports “Syntax is ok”.
Page 220 • t[#] n’th input trace. Access the input trace (data wave) in Scope channel position “n” for the last sweep of the current Series. This numbering can differ from the Scope Position "n", if signals are re-arranged or hidden. Tip: You can duplicate an input signal with this.
Page 221 current, which is then used to correct the P/N leak average. This option reduces the influence of a constant leak-current, which is otherwise added to the leak current of the main pulse. Enable LineFreq Remove AC line frequency noise (hum) from the data signal. •...
Page 222 Current Channel Select a (source) input channel with a “current” signal. Trace Kind Select the LockIn measurement to display. The selected ‘Trace Kind’ is automatically set as the Virtual Channel label. Computed membrane capacitance. Computed membrane conductance. Computed series conductance. DC component of measured signal.
Page 223 # of smoothing operations to perform. Boxcar A fast time-domain filter with excellent 0 • – 100% rise-time response. Smooth Repetitions [ 1 – 32767 ] # of smoothing repetitions to perform. Boxcar Window Points [ 1 – 99 ] # of points in boxcar sliding window.
Page 224 sweeps. Number of Sweeps [ for Run Average ] Start Sweep Sweep number to start sweep averaging. Set Sweep < Start Sweep To NAN Sweeps prior to the Start Sweep are set by default to the initial source sweep. Enable to set these pre-sweeps to NaNs. End Sweep Sweep number to end sweep averaging.
Page 225: Output Channels & Waveform
Output Channels & Waveform Configure the output channels and command waveforms. Figure 4-58. Output Channels & Waveform [ Status field ] Hardware information displays for the highlighted channel. Digital Outputs set as The digital output channels (bits) can be set individually or as a group. Individual bits DigOUT[1 –...
Page 226 ‘HIGH’, it has a ”word” value of 4. 16-bit Word [ 0 – 65,535 ] • The 16-bit digital output pattern is controlled by a single decimal number, which is also the waveform preview amplitude value. The waveform preview uses the binary bit pattern decimal word value for its Y-axis value, i.e., if bits 1 and 3 are ‘HIGH’, the word has a value of 5.
Page 227 Label A user-defined signal name for the channel. These are used in: ‘Copy Channel’ • Waveform Preview pane ‘Show Channel’ • Metadata: Output Signal Name • To rename an Output Channel, first enable it, then double-click its Label field and enter the new name.
Page 228 recording modes. Unit [ read-only for StimOUT channels ] Fixed at ‘V’ for voltage-clamp experiments, and ‘A’ for current-clamp. [ editable for AuxOUT channels ] Enter the base unit of measurement from a drop-down list. The signal’s unit resolution is automatically adjusted. Or edit the text field to add new nomenclature to the list.
Page 229 Amplifier Control Panel. If the holding level is set to ‘0’, this setting has no effect. Relative to I/O Setting AuxOUT For the Auxiliary channels, the command waveform is summed with the Amplifier Control Panel I/O ‘Auxiliary Output’ settings. DigOUT For digital channels, the command waveform is relative to the Amplifier Control Panel I/O ‘Digital Output’...
Page 230 • Return to Holding Set the output signals to the Amplifier Control Panel “holding” levels, at the end of a Routine. This ensures that your cells are kept in a resting state as much as possible. Note: In demo mode, after changing holding levels, if ‘Relative to Holding’ is enabled, then the ‘Return to Holding’...
Page 231 Enable P/N Leak Pulses Displays the P/N Leak Pulses section. Figure 4-59. Output Channels & Waveform with Leak Endogenous leak currents can flow, even while a cell is in its resting state, from conditions such as an imperfect or leaky seal, or via existing ion channels, and affect response amplitudes.
Page 232 (e.g., with voltage-gated sodium currents), click ‘Enable P/N Leak Pulses’ and configure its settings below. A “leak pulse” is a replica of the stimulus waveform, and is used to record a fraction of the leakage current. In this technique, leak pulses are generated, and the responses are averaged, scaled, and subtracted from the main response to remove the effects of leakage.
Page 233 interdependent. Tip: As an alternate way to avoid electrical activation of ion channels, use a negative ratio to reverse the polarity of the leak pulses relative to the main pulse. Leak Hold The leak pulses holding level can be set differently from the Routine main holding level, for flexibility in finding a suitable leak pulse voltage range.
Page 234: Waveform Editor
When leak pulses occur before the main pulse, Leak Delay uses the amplifier’s Holding level; when leak pulses occur after the main pulse, Leak Delay uses the Leak Pulses ‘Leak Hold’ level. Enable A/C Line Frequency adjustment The effect of AC line-frequency noise (hum) can be automatically reduced during P/N leak subtraction recording: 60 Hz Enable the reduction of 60 cycle AC line noise.
Page 235 pattern. Only displays settings for Bit Word “Values” (not for lists, increments, etc.) Used segments: [ # out of 50 ] Displays how many of up to 50 contiguous Segments are configured in the waveform. Actions Unused Segments are labeled as ‘OFF’. Tip: A Segment with a Duration of ‘0’...
Page 236 Any following Segments shift their Segment #’s down by the number of deleted Segments. Waveform Select the waveform shape. For Waveform types Sine / Chirp / Squarewave / Template / Triangle, a ‘Parameters’ field displays below this field, to allow quick access to their parameters.
Page 237 Multiple sine LockIn Segments in a waveform share the same settings (except duration) for each Segment. Amplitude [ ±0.75 V, ±20.0 nA ] Amplitude of the first peak from the sine wave baseline. Value • Var_r[1] – [16] • Tip: To offset a sine wave from the default baseline (0 units), set the Segment...
Page 238 Not enabled for a Single cycle. Segment Duration Sine wave duration (ms). Square Pulses The waveform generates a train of rectangular pulses. Base Amplitude Increment [ ±0.75 V, ±20.0 nA ] Increment the baseline amplitude for each succesive pulse. Step1 Amplitude [ ±0.75 V, ±20.0 nA ] Amplitude of first pulse.
Page 239 chirp, a minimal frequency spread is enforced: the End Frequency has to be at least double the Start Frequency, or half or less of the Start Frequency. Amplitude [ ±0.75 V, ±20.0 nA ] Start Frequency [ 1 – 50000 Hz] End Frequency [ 1 –...
Page 240 Template Editor Pool Lists the templates loaded in the Template Editor, plus any extracted templates. Copy the selected template wave from the Tem- plate Editor Pool into a Routine and Segment. This button is enabled if the ‘Number of Sweeps’ allows more Segment templates.
Page 241 If multiple templates are copied into the Routine Segment, they will be executed in sequential or- der, one template per sweep. Sweeps Number of sweeps in the Routine. Sweeps are assigned to templates in sequential order. If the number of sweeps is greater than the number of templates, the sweep number cycles back to the first template and continues incre- menting the templates, etc.
Page 242 Ramp2 Width Duration of the secondary phase. Frequency [ read only ] Segment Duration Duration of the triangle train. Membrane Test The Membrane Test runs in ‘Cell’ mode. The waveform applies a predefined negative pulse step (-5 mV) with a 50% duty cycle for Routine-based measurements.
Page 243 Value [ ±0.75 V, ±20.0 nA ] Use a single number for the Segment amplitude. Value List Set an arbitrary Segment amplitude for each sweep. [ Sweep | Value ] [ # | ±0.75 V, ±20.0 nA ] For each numbered sweep, enter a value.
Page 244 Insert special identifier Acquisition, amplifier and reference settings are available for use in equations. (See list in Equation Editor.) Undo All changes in the equation editing session are discarded. (See the Equation Editor for more details.) Warning! Computing an equation for a command waveform con- sumes significant computing power, as every data point needs to be computed by the CPU.
Page 245 a value. (Blank lines are removed.) Fill Remaining List Copy the active value to all remaining sweeps in the list. Number of Sweeps Adjust the number of sweeps in the Routine. Value+Increment Increment the Segment duration for each sweep. Start value [ ms ] Increment value [ ms ]...
Page 246 table is enabled. Segment Controls To copy or delete a Segment, click on its background area, and its color turns gold. This enables the additional Actions items: Copy and Delete. Standard mouse behaviour is used to select multiple Segments: Individual Segments: Windows: Ctrl-click •...
Page 247: Real Time Measurements & Graphs
Real Time Measurements & Graphs Online analyses are configured in the Real Time Measurements & Graphs dialog. Measure- ment regions display in the Acquisition: Routine Scope window, and their associated analyses are plotted in an Analysis sub-window during acquisition. Figure 4-62. Real Time Measurement Settings Disable Execution of Measurements and Graphs Block execution of all measurements and analyses with one click.
Page 248 Clear All Measurements All measurements and their settings are cleared. Analysis Be sure to set appropriate Region Timing (below) for the following analyses. Analysis Function Select a predefined Analysis statistic for each measurement: Absolute area Negative area values are converted to positive and summed with the positive area values.
Page 249 RMS noise Root-Mean-Square noise. Segment amplitude Amplitude of the specified ‘Out Chanel’ Segment. Segment duration Duration of the specified ‘Out Channel’ Segment. Slope Slope of a simple linear regression fit. Std deviation Standard deviation of the samples: √(variance) Stimulus at absolute peak Stimulus amplitude at time of the largest absolute sam- ple.
Page 250 Rise/Decay time • Rise/Decay Tau • Frequency • Time to threshold • Polarity The direction of a Threshold crossing. Positive Positive-direction threshold crossing. • Negative Negative-direction threshold crossing. • Largest change Use the polarity direction of the largest change for •...
Page 251 Signal to Analyze For each enabled Analysis measurement, select which signal is to be measured from the list of Input Channels. "Membrane Test" signals are restricted to the headstage “Current” inputs. A measurement made on one input channel can be used in multiple graphs. Region Timing Cursors Relative to Set the measurement boundaries with left / right cursors.
Page 252 Fix the width of the measurement region. The measurement width is maintained at a con- stant value when the cursor ‘Start Time’ is up- dated. ] The width of the cursors in seconds. The minimum width size is 2 sample points.
Page 253 Cursor Time Width The width of the measurement region is reported. Graph Settings Figure 4-63. Real Time Graphs Enable a graph to configure its settings. Graphs have a default ID (identification): g[1] - g[8] Show Display this graph in an Analysis window during acquisition and analysis. Note: If the Y-Axis ‘Equation’...
Page 254 Analysis measurement, by using Special IDs in the equation. <m[#]: Name> Select a Measurement ID for the X-axis. • Label A Y-axis label is automatically generated from the Measurement label. Directly edit to customize the Y-axis graph label. Unit Select a standard unit from the drop-down list, or enter a custom unit type.
Page 255: Routine Editor: Routine Variables
Routine Editor: Routine Variables Up to 16 Routine Variables can be configured for use in Routines. These variables allow manual or automatic control of certain Routine settings. Figure 4-64. Routine Variables Routine Variables In Use A checkmark means the Routine Variable is “active”, i.e., set to a non-zero value, or is being used in a Routine setting or equation field.
Page 256: Solution Editor
Measurements / AP Duration / Threshold Measurements / Frequency / Threshold Measurements / Time to Threshold / Threshold If a Waveform Editor ‘Amplitude’ or ‘Duration’ is set to a Routine Variable, and then changed to a value, the Waveform Editor converts its ‘Var_r[#]’ settings to ‘Value’ settings, using the last enabled value.
Page 257 Revert to Last Saved Undo any unsaved changes to the Solution Pool. Save Solution Pool Save the Solution Pool using its existing filepath. Save Solution Pool As Save the Solution Pool to a new file, and switch to the new file. Save Solution Pool Copy Save the Solution Pool to a new file, but do not switch to the new file.
Page 258 [ Solution Type list ] A list of predefined solution types. Initial Condition • Washout • Control • Index [1 – 4] Distinguish between different Control solutions. Test Compound • Not a Solution • [ Output Channel ] Select a physical output channel and set its value. No Output •...
Page 259: Template Editor
Template Editor SutterPatch: Template Editor Templates allow any data waveform or portion of an existing data wave to be incorporated into a command waveform. The Template Editor can manage and manipulate such templates. Figure 4-66. Template Editor Note: Changes made in the Template Editor are only applied to Routines when the Routine Editor / Output Channels / Waveform Editor / ‘Template wave’...
Page 260 Save Template Pool As Save the Template Pool to a new file, and switch to the new file. The default file name is the same as the original file name. Save Template Pool Copy Save the Template Pool to a new file, but do not switch to the new file.
Page 261 Delete Remove the selected template from the list. Copy to Layout Copy the selected template graph into a new Layout window, or append to an existing Layout page. Copy to Clipboard Copy the selected template graph to the system clipboard. Save Pool Save the template pool using its existing file name.
Page 262: Data Analysis
Do It Apply the adjustments to the template parameters. Template Names A list of the loaded templates. Click on a Template entry to make it the active one. Double-click on a Template Name to rename it. Click-and-drag a Template entry to reposition it in the list. Template Parameters Parameter settings description.
Page 263 Fitting can be applied to most displayed data. Offline data processing is performed in the Analysis Editor: Average • Concatenate • Normalize • Offline analysis modules are provided via the Data Navigator ‘Available actions’: Action Potential Analysis • Single-Channel Analysis •...
Page 264: Action Potential Analysis
4.2.1 Action Potential Analysis SutterPatch: Available Analysis Modules: Action Potential Analysis Action potentials (APs) are analyzed offline with this window. Access via the Reanalysis Scope window ‘Measurements’ button or the Data Navigator (signal) ‘Available actions’ menu. Figure 4-67. Action Potential Analysis Sweep # The sweep number of the selected action potential event.
Page 265 Event Time Time point when the potential of the selected event crosses the thresh- old. [ Event pane ] A graph of the selected event, with the X-axis zero point reset to the Threshold point. To measure X-Y data points or set a fitting range, select ‘Toggle Cursor Info’...
Page 266 Analysis Start (s) [ 0+ ] Set the start-time of the Sweep data to be analyzed. Analysis End (s) Set the end-time of the Sweep data to be analyzed. Save Results The latest results are displayed in the ‘Action Potential Analysis Results’ Layout window and a Results table window.
Page 267 ‘Action Potential Analysis Results’ Layout window Signal Pathname: The Igor Pro experiment pathname for the analyzed signal. Analysis Prefix: The prefix for the signal’s analysis objects in the Igor Pro ‘Data:Analysis' folder. Total time analyzed = [ s ] Includes the Start / End times for all analyzed sweeps. Number of events detected = Total number of events found.
Page 268 Results pane Measurement results are displayed for the event selected in the main window. Figure 4-68. Action Potential Measurements Phase plot A graph of the phase plot, for visual inspection of the derivatives. [ dV/dt (V/s) vs. V ] Y-axis vs. X-axis. To measure X-Y data points or set a fitting range, select ‘Toggle Cursor Info’...
Page 269 Action Potential Duration of the event at (n %) of amplitude re- polarization. AHP (min) = [ V (s) ] The largest amplitude excursion of the “After HyperPolarization” phase of the event (time from ‘Threshold’ setting). Two measures of the AHP amplitude are reported, voltage and time.
Page 270: Analysis Editor
4.2.2 Analysis Editor SutterPatch: Analysis Editor View and manipulate the data in your Experiment’s various analyses and graphs Figure 4-69. Analysis Editor Select Choose how to view the data. Table View a spreadsheet of the Analysis data. Warning! Editing the table will permanently alter its data. Tip: As there is no “Undo”, before making any changes, use Operations / Duplicate to make a working copy of the data...
Page 271 Columns for time-based graphs First Column: Row numbers. Second Column: “X \ Y” column label. [ has blank rows ] Column 0: X-data (Time) from the first graph: start times of the measurement sweeps. Column 1: Y-data from the first graph: amplitudes of the measurements.
Page 272 Files Import or export an analysis graph file. Export Table to text file The table data are written to a tab-delimited plain text file. Any column header information is lost. To preserve such metadata, export to the binary format. Export Graphs as binary wave Save the entire graph as a multi-dimensional Igor Binary Wave file (*.ibw).
Page 273 Options Show Fits Display fit lines on the graph data. Show Error Bars Display SEM error bars for averaged data. Show Axes Color Display a background color for the axes. Show Grid Display X & Y grid lines in a graph. Show Markers Display data points with marker symbols.
Page 274 wave. A weighted average is performed, i.e., the number of data sets is accounted for when averaging in new data. Two new entries are inserted into the wave list after the loaded wave: 1. The averaged wave. 2. The SEM (Standard Error of Means) data points wave. If ‘Options / Show Error Bars’...
Page 275 Cursor Info pane Options menu One Mover Moves All • Draggable cursor mover tool – move all cursors together with a single control. All Styles Change the cursor symbol style. • Show Cursor Pairs Display up to 5 sets of cursor symbol pairs. •...
Page 276 ΔX Difference of the cursor pair X values. Cursor Instructions 1. Click on symbol ‘A’ to enable it. 2. Manually drag the highlighted symbol onto a data point in the graph, or en- ter the data point number in the ‘pnt’ field. 3.
Page 277: Analysis Window
4.2.3 Analysis Window Scope measurements are plotted in an Analysis window docked on the right side of the Scope window. An Analysis window can be resized or closed, but not undocked from the Scope win- dow. Figure 4-70. Analysis Window Online measurements are plotted during data acquisition in real-time.
Page 278 Copy to Clipboard Copy the analysis graphs to the system clipboard. [ Graph panes ] The Graph pane X- and Y-axes can be magnified to be larger or smaller. Place the mouse cursor in an axis tick region (do not include the tick labels or numbers), then scroll the mouse wheel up or down.
Page 279 Y-axis value of data point ‘A’. ΔY Difference of the cursor pair ‘Y’ values. Cursor B Cursor symbol for data point ‘B’. Symbol letter (ending cursor of the A/B pair). R1_A_IV (Default) wave name. Draggable cursor mover tool for the cursor pair. pnt: Data point number (starting from zero).
Page 280: Data Browser
4.2.4 Data Browser Data: Data Browser The Data Browser can be used to access and display all of the Experiment’s data objects, such as recorded data waves, analysis graphs, layouts, images, metadata, Paradigms and Routines. Access it from the Data menu. Figure 4-71.
Page 281 For the macOS: opening and closing windows can take a long time. The ‘Data’ subfolder contains additional subfolders, followed by recorded data waves arranged per Signal. ExperimentStructure The sequence of Paradigms and Routines. <Names of data Series…> Analysis This folder contains data measurements, including results from fits, and Event tables.
Page 282: Data Navigator
4.2.5 Data Navigator SutterPatch: Data Navigator The Data Navigator window organizes and displays all levels of data for the current Experiment. Figure 4-72. Data Navigator Data tree hierarchy The hierarchy of sorting levels is displayed in this pane. Build Hierarchy Re-organize the data tree using custom settings.
Page 283 Experiment Hierarchy Operator Preparation - Animal Preparation - Tissue Preparation - Cell Experiment Amplifier Instrumentation and Software Electrode Recording Solutions Paradigm Cell Health / Quality Control Series (= Routine Data) Data Acquisition Settings Imaging Stimulus Available parameter Click on a specific parameter from the selected group. Click on the “copy”...
Page 284 Data Tree Window The current Experiment’s data are arranged in the data tree in five default levels: Experiment Paradigm Routine Signal Sweep Selecting a node level in the data tree highlights it in blue. Enable Marks Allow data to be marked in the data tree or Available Actions menu for analysis processing.
Page 285 Collapse All All nodes of the data tree are collapsed up to the Paradigm level. To collapse the lower levels of a node, with a mouse click on a “-” node, or double-click the node name; with a keyboard, use the up/down arrow keys to select a “-”...
Page 286 Don’t subtract zero-current from traces • Subtract zero-current from traces • Set Defaults Import pClamp Data File • [ This option is only available if Sutter Amplifier Systems hardware has been attached and detected by the SutterPatch software at any previous point in time for the current OS user.
Page 287 Note: The Data Navigator Preview panes do not support mouse operations. Experiment Experiment Name: The experiment file name. HDF5 File Name: For optional HDF5 files. Paradigms: Total number of Paradigms in the Experiment. Routines Total number of Routines in the Experiment. Total bytes in data waves: Combined size of all data waves in the Experiment.
Page 288 Routine: Click to display the named Routine’s parameters. Analysis: Click an analysis name to open it into the Analysis Editor. Signals: Number of signals in the Routine. Sweeps: Number of sweeps in the Routine. Images: Open any saved images. The image preview window text Note is editable.
Page 289 Review is Sweeps Display Mode Review in Concatenated Display Mode Review in Time Course Display Mode Available Actions button A menu lists various actions for the marked and/or highlighted data levels. These actions are also available via a right-click on the selected data level. Experiment Copy Signal Data Paths Copy the Series internal Igor Pro...
Page 290 Copy Analysis Graphs to Layout Page [ the following options display when ‘Enable Marks’ is checked ] Mark All Paradigms All Paradigms in the Experiment are marked. Unmark All Paradigms All Paradigms in the Experiment are unmarked. Mark All Routines All Routines in the Paradigm are marked.
Page 291 Check the equation syntax. The equation is evaluated, and if valid, it reports "Syntax is ok.” Insert special identifier sweep Enumerate the sweeps in the equation when applying marks. Odd( sweep ) Set all odd sweeps to “1”, and all even sweeps to “0”.
Page 292 View Metadata Display the highlighted Paradigm’s metadata in the Metadata Review sub-window, docked to the right of the Data Navigator window. View Paradigm Steps [ only displays if ‘Enable Marks’ is disabled; only executes for “planned” Paradigms ] Display the steps from the selected Paradigm in a ‘Paradigm Steps Review’...
Page 293 Choose a different folder, or First delete the older file via the OS file browser. ------------ Discard Paradigm Remove the highlighted Paradigm and its data from the Experiment. If marks are enabled, the selected Paradigm also needs to be marked. If the last Paradigm is discarded, when acquiring another Paradigm in the same...
Page 294 Mark All Signals All signals in the Paradigm are marked. Unmark All Signals All signals in the Paradigm are unmarked. Mark All Sweeps All sweeps in the Paradigm are marked. Unmark All Sweeps All sweeps in the Paradigm are unmarked. Set Routine Marks by Name Match Opens the ‘Routine Mark: Name Match Editor’...
Page 295 sweeps to “0”. Even( sweep ) Set all even sweeps to “1”, and all odd sweeps to “0”. Do Mark Evaluate the equation and update the sweep marking. [ Status message ] value >= 0.1 = 1 (marked) value < 0.1 = 0 (unmarked) Routine Analyze Routine Display the marked sweeps of all...
Page 296 Changes are appended to the metadata as tags. Copy Signal Data Paths Copy the Series internal Igor Pro path to the system clipboard: root:SutterPatch:Data:Series_na Show in Data Browser Open Igor Pro’s Data Browser window to examine the highlighted Series’ data waves. Export Data (See Preferences) Export the marked Series to file(s).
Page 297 Restore concatenated Sweeps Convert the concatenated sweep back to the original sweeps. Change Sweep Duration Restore Sweep Duration ----------- [ the following options display when ‘Enable Marks’ is checked ] Mark All Signals All signals in the Series are marked. Unmark All Signals All signals in the Series are unmarked.
Page 298 in the equation when applying marks. Odd( sweep ) Set all odd sweeps to “1”, and all even sweeps to “0”. Even( sweep ) Set all even sweeps to “1”, and all odd sweeps to “0”. Do Mark Evaluate the equation and update the sweep marking.
Page 299 Marked signal: Display all sweeps in the signal in a graph window. Average All Sweeps Average all sweeps in the highlighted signal and display in the Analysis Editor. Average Marked Sweeps Average the marked sweeps in the highlighted signal and display in the Analysis Editor.
Page 300 Choose a different folder, or First delete the older file via the OS file browser. ------------ [ the following options display when ‘Enable Marks’ is checked ] Mark All Sweeps All sweeps in the Series are marked. Unmark All Sweeps All sweeps in the Series are unmarked.
Page 301: Data Table
4.2.6 Data Table The Data Table provides direct access to the sample points in a data Series, using a spreadsheet-style presentation. Figure 4-73. Data Table Warning! Editing data permanently alters the raw data. Modify at your own risk! Data Tables are accessed from the Data / Data Browser. Select a Series from the Data folder, then right-click the menu item ‘Display’.
Page 302 Figure 4-74. Edit Virtual Signals Virtual Signal Parameters from [ <Series name> (date/time stamp) ]  Overwrite with Original Routine  -------------- Source Signals Label The input signal name. DPATCH – OPERATION MANUAL – REV. 2.3 (2022-10-24)
Page 303 New Label Double-click this field to edit the signal name, then click the 'Do It' button. Legal characters are A-Z, a-z, 0-9, and underscore “_”. The label must start with a letter, be at least two characters long, and not be a duplicate of another label.
Page 304 Unit The base unit of measurement from its Source signal. The resolution of the unit is automatically adjusted in the signal. Parent Out Chan The “Parent Output Channel” shows which output channel is associated with which input channel. -------------- Scope Position Signal Action None •...
Page 305 Filter Bandwidth The input-channel low-pass 8-pole Bessel filter bandwidth. Nyquist Factor To manage the quantity of data being processed, the hardware headstage sampling rate is downsampled from an initial fixed 5 MHz rate to a “Nyquist Factor” mulitple of the ‘Filter Bandwidth’: The sampling rate is set to twice (2x) the filter rate;...
Page 306 Trace Subtract the average of the entire input • trace. Sweep Time Subtract the average of the data between • the Start Time and End Time. Start Time Set the starting time of the data to be averaged. End Time Set the ending time of the data to be averaged.
Page 307 Filter Order [ 1, 2, 4, 8 ] Number of “poles” in the filter. Cutoff Frequency (Hz) [ 100 to < ½ the sampling rate ] Restrict frequencies from this boundary point onwards. Integrator Reset [ for Capacitive Mode ] Ignore Capacitive-mode transients are •...
Page 308 Source Channel Select an input channel to process. Equation [ Click field to access the ‘Specify math equation’ editor. Note: The full equation is always visible as a tool tip, by hovering the mouse cursor over the ‘Math Equation’ field. Specify math equation for virtual signal [ <equation>...
Page 309 The current series, current sweep, current trace, of the current routine. t[#] nth input trace. • Access the input trace (data wave) in Scope Position “n” for the last sweep of the current Series. This numbering can differ from the Scope Position "n" if signals are re-arranged or hidden.
Page 310 The mean of the second half of the specified Segment is used to compute an averaged leak current, which is then used to correct the P/N leak average. This option reduces the influence of a constant leak-current, which is otherwise included in the current of the main signal.
Page 311 display. The selected ‘Trace Kind’ is automatically set as the Virtual Channel label. Computed membrane capacitance. Computed membrane conductance. Computed series conductance. DC component of measured signal. RealY Real number part of the lock-in response signal. ImagY Imaginary number part of the lock-in response signal.
Page 312 perform. Boxcar A fast time-domain filter with • excellent 0 – 100% rise-time response Smooth Repetitions [ 1 – 32767 ] # of smoothing repetitions to perform. Boxcar Window Points [1 – 99] # of points in boxcar sliding window. Note: For best performance, only odd values are used.
Page 313: Equation Editor
Source Channel Select an input channel to average. Average Type Cumulative Average all processed sweeps together. RunAverage Average the last “N” sweeps. Number of Sweeps [ for Run Average ] Limit to Marked Sweeps Enable to limit this analysis to marked sweeps.
Page 314 Figure 4-75. Equation Editor Equation Pool Files Equations are created and saved in an Equation Pool file. New Equation Pool Create a blank Equation Pool file. Load Equation Pool Load the Equations of a previously saved Equa- tion Pool file into the Equation Pool. Revert to Last Saved Undo any unsaved changes to the Equation Pool.
Page 315 Save Pool Save the Equation Pool using its existing file name. Edit Make edits to the ‘Equation’ field. Check Equation The equation is evaluated (for sweep #1), and if valid, it reports “Syntax is ok”. Insert special identifier SutterPatch acquisition, analysis and reference settings are available for use in equations.
Page 316 ForEachSweep EachSweep, Target=IV If, Left=sweep, Operation= ‘=’, Right=LastSweep-1 Alert, Text=LastSweep, DoBeep=true EndIf ForEachEnd AqStopped (last acquisition was stopped) The last Routine-Series did not complete by itself. Stimulant (last applied stimulant concentration) From the Solution Editor ‘Concentration’ setting for solutions configured as a ‘Chemical Stimulant’. Input (Input variable on paradigm window ) Hold[1..2]...
Page 317 In the Amplifier Control Panel (mV). Mean[name or count, start,width] (mean of given input signal) Headstage ActiveProbe (active headstage) [ 1 – 2 ] The “active” probe number is the Sutter headstage presently controlled by the Amplifier Control Panel. For a single headstage system, the active probe is always headstage number "1".
Page 318 Read the gain of the active voltage-clamp ‘Current’ input channel. VGain (amplifier voltage gain, V/V) Read the gain of the active current-clamp ‘Voltage’ input channel. Feedback (amplifier feedback mode: 0, 1, 2) Filter (amplifier input filter in VC- and CC- mode, Hz) Read the filter of the appropriate input channel in either VC- or CC-mode.
Page 319 ECompMag (amplifier electrode compensation magnitude, F) ECompTau (amplifier electrode compensation tau. s) ECompOn (amplifier electrode compensation On in CC-mode) CmComp (amplifier cell compensation Cm, F) RsComp (amplifier cell compensation Rs, Ohm) RsCompOn (amplifier cell compensation On) Bridge (amplifier bridge balance, Ohm) BridgeFraction (amplifier bridge balance, fraction of Rs) BridgeOn...
Page 320 DynHold (amplifier dynamic holding potential, V) DynHoldSpeed (amplifier dynamic holding speed) DynHoldAqOn (amplifier dynamic holding active while acquiring) Membrane Test Relectr[1..2] (electrode/seal/access resistance, Ohm) Value from last Membrane Test. Rmemb[1..2] (membrane resistance (cell mode), Ohm) Value from last Membrane Test. Cmemb[1..2] (membrane capacitance (cell mode), F) Value from last Membrane Test.
Page 321 The "X" (or “x”) specifier allows an argument to be passed to an equation. Insert “X” as the placeholder(s) in numeric expres- sions. To call such an equation in other parts of the program, prepend a “#” to the equation label, and append the argument in parenthe- ses.
Page 322 Lists Anywhere equations can be used, a list of comma-separated equations can also be used, to generate a sequence of values. If the sequence extends beyond the end of the list, the sequence wraps around and continues from the beginning of the list again, and so on.
Page 323: Table 4-4. Equation Parser
Equation parsing is executed from left to right, processing the highest prece- dence level operators first, except for comparison and bitwise operators, which associate from right to left. Precedence Operation Type Operator Comment Exponentiation, Arith- ^, <<, >> metic operations: Left Shift, Right Shift Negation operations: -, !
Page 324 A semicolon separates multiple commands on the same command line. An arithmetic left shift (<<) is the same as a bitwise left shift, whereby the least significant bit is padded with a zero. However, while an arithmetic right shift (>>) fills the most significant bit with its original value, thus preserving the sign, a bitwise right shift pads the most significant bit with a zero.
Page 325: Table 4-5. Engineering Notation
Prefix Prefix Prefix Exponent Name Prefix Exponent Name Kilo milli Mega µ (or u) micro Giga nano Tera pico Peta femto atto Zetta zepto Yotta yokto Table 4-5. Engineering Notation Insert an equation from the Equation Editor Pool into an Equation field •...
Page 326: Igor Pro Analyses
Routine Editor Input Channels: Virtual Channels: Math Type: Equation Output Channels: P/N Leak Pulses: Leak Hold; Waveform Editor: Ampli- tude, Duration Measurements: Time to Threshold, X-Axis, Y-Axis Note: For acquisition, computing an equation within a a command waveform consumes signif- icant computing power, as every data point needs to be computed by the CPU.
Page 327 Sigmoid Use for Boltzmann function. Power LogNormal poly2D [ 1 – 10 ] Gauss2D -------------- Fit Between Cursors Weight from Error Bar Wave Textbox Preferences Example: Perform a fit on a section of a sweep: Open the data into a Reanalysis Scope window. In the Scope window, right-click ‘Toggle Cursor Info’...
Page 328: Metadata Review
• Filter • Resample • Sort • Histogram • Compose Expression • Packages Average Waves  Batch Curve Fitting  Function Grapher  Global Fit  Igor Filter Design Laboratory  • Median XY Smoothing • MultiPeak Fitting • Percentiles and Box Plot •...
Page 329 Open a Series into a Reanalysis Scope window (from the Data Navigator ‘Analyze’ button or Action ‘Analyze Routine’), and use the ‘View Metadata’ button to open a Metadata Review floating sub-window. To simultaneously display metadata from two different Paradigms, use floating and docked windows: Select the first Paradigm and the Action ‘Review Paradigm’.
Page 330 Expand All All settings entries are displayed. Two columns of information are presented (parameter name and value). If the first column’s text does not fully display, either increase the width of the window, or adjust the indentation of the second column by dragging it when the mouse cursor turns into a double-headed arrow.
Page 331 Interface Signal Type Interface Number of Digital Outputs Computer Name Physical Computer Memory Operating System Platform Operating System Software Environment Software Environment Version Software Environment Build Software Environment Kind Software Environment Serial Number Data Acquisition Software Data Acquisition Software Version Data Acquisition Software Build Data Acquisition XOP Version Paradigm...
Page 332 Input Scaling Offset Input Full-scale Minimum Input Full-scale Maximum Input Sampling Rate Auxiliary Input Signal Offset [ for AuxIN channels] Virtual Signal Scaling Offset [ for Virtual Input channels ] Virtual Signal Math Type [ for Virtual Input channels ] Virtual Signal Equation [ for Virtual Input channels ] Virtual Signal Source Channel...
Page 333 Dynamic Clamp Model [ CC mode, if DynClamp Active ] Command Signal Name 1 Command Signal Unit 1 Command Full-scale Minimum 1 Command Full-scale Maximum 1 Command Sampling Rate 1 Command Holding Enabled 1 Command Holding Value 1 [ ‘0’ if Holding disabled ] Auxiliary Output Signal Name 1 [ if AuxOUT1 enabled ] Auxiliary Output Scaling Factor 1...
Page 334: Paradigm Review
Compound Counterion Compound Source Compound Solution Compd. Vehicle / Solubility Enhancer Compound Vehicle Concentration Compound Vehicle Conc. Unit Compound Reservoir Identifier 4.2.11 Paradigm Review ‘Paradigm Review’ displays data from all Series within the Paradigm in a modified reanalysis Scope window, in a Time Course or Concatenated view. This view also displays tags that occur between Series.
Page 335 Figure 4-76. Reanalysis Measurements & Graphs This dialog operates similarly to the Routine Editor: Real Time Measurements & Graphs dialog, with the addition of optional configurations: DPATCH – OPERATION MANUAL – REV. 2.3 (2022-10-24)
Page 336 Measurement Parameters from The name of the Series data, and the date/time of the last update to the Measurement parameters. The current parameters can be optionally overwritten (updated) from these sources: • Overwrite Measurements from Original Routine • Overwrite Measurements with Active Values The last run analysis values are remembered.
Page 337: Reanalysis Scope
4.2.13 Reanalysis Scope This analysis version of the Scope window is used to display and reanalyze stored data. Figure 4-77. Reanalysis Scope Window Both physical and virtual channels can be displayed and analyzed here. Many window controls are the same as in the ‘ Routine’ Scope window, however others have slight changes, and new controls were also added: Navigation pane The Navigation pane appears at the top of the Reanalysis Scope window.
Page 338 Figure 4-78. Navigator Pane The Navigation pane “magnification” box can be used to scroll through the active sig- nal’s data. Place the mouse cursor over the magnification box and it changes into a ‘hand’ icon; click and drag the magnification box to move it around the data of interest. Buttons Scope Settings: Show all sweeps...
Page 339 Show Cursors: Display measurement cursors in the Scope window. Hide Cursors: Do not display cursors in the Scope window. Button displays as “Measurements(H)”. Lock Cursors: Prevent cursors from being adjusted or moved. Button displays as “Measurements(L)”. No Measurements or Graphs Analyze with Active Measurements Analyze with Original Routine Measurements Analyze with Routine Last Executed Measurements...
Page 340 Amplitude Histogram Plot Plot an amplitude histogram. (see below) Color Plot Map the data to a color table. (see below) Display any extra information (metadata) associated with the dis- played data Series, such as the operator, preparation details, solu- tion information, etc., in a floating window. Open a Data Navigator window with all of your Experiment data and metadata available for analysis in a tree structure.
Page 341 Applies to the Scope window, and its (right-click) graphs: Parametric Plot and Amplitude Histogram Plot. Graphically arrange the input signals. Signal Layout Stack: A vertical column of signals. Single: Only the active signal. m x n: A tiled array of signals with ‘m’ rows and ‘n’ columns. Sweeps Display This button has 3 modes: Sweeps...
Page 342: Table 4-6. Reanalysis Scope Window Buttons
The ‘Show 3D view of current signal’ button brings up a separate 3D display window attached to the right of the Analysis window. The Sweep data are color-coded for amplitude, and their 3D graph can be rotated in any direction. (see below) The ‘Sweep #’...
Page 343 If this window is left open when the Scope window is closed, it will also close; and re-opening the Scope window will also re-open the Parametric Plot window. Y-signal Select an input signal for the Y-axis. X-signal Select an input signal for the X-axis. Plot Update the plot using the new parameters.
Page 344 Set the ending time ratio. Measurements can be made on the parametric graph using Igor Pro cur- sors (Ctrl-I). The cursor measurement is written to the SutterPatch Notebook window. Amplitude Histogram Plot Open a histogram plot window. The amplitude data is binned and plot- ted.
Page 345 Copy the Amplitude Histogram Plot graph to the system clipboard. Cityscape Display the plot line using steps, no interpolation. Plot Refresh the plot for any Time Range settings changes. [ graph pane ] Measurements can be made on the amplitude histogram graph using Igor Pro cursors (Ctrl-I).
Page 346 Copy to Layout Copy the Color Plot graph into a new Layout win- dow, or append to an existing Layout page. Copy to Clipboard Copy the Color Plot graph to the system clipboard. Measurements can be made on the color graph using Igor Pro cursors (Ctrl-I).
Page 347 Set Y Scale… Manually set the Y-axis range. Y-min The Y-axis minimum value. Y-max The Y-axis maximum value. Copy Y scale of signal [ input signals list ] Apply the Y scaling from another signal. Axis Properties… Modify the axis style and components. To reverse the Y-axis polarity (such as for inside-out or cell-attached patches)…...
Page 348 Main Window Limited data modification menu Right-click in the blank area in a signal pane. Tip: If you click too close to the signal data, the full data modification menu displays instead if this occurs, click near a horizontal or vertical edge of the signal pane.
Page 349 Show Signal ‘<name>’ Only Show the selected signal in the Scope window, and hide all other signals. Show Last Sweep of ‘<name>’ only Display only the last [marked] sweep of the se- lected signal. Show All Sweeps of ‘<name>’ Restore the display of all [marked] sweeps in the selected signal.
Page 350 Set Time Range of Amplitude Histogram [ only in Scope if an Amplitude Histogram is open ] Set Time Range of Analysis [ only in Scope if Single Channel Analysis is open ] Set Time Range of Parametric Plot [ only in Scope if a Parametric Plot is open ] Signal Data Full data modification menu Right-click on or near the data to display this context menu, which includes op-...
Page 351 Show Cursor Pairs Display up to 5 sets of cur- • sor symbol pairs. Cursor A Cursor symbol for data point ‘A’. Symbol letter (beginning cursor of the pair). R1_A_IV (Default) wave name. Draggable cursor mover tool for the cursor pair. pnt: Data point number (starting from zero).
Page 352 4. Manually drag the highlighted symbol onto a data point in the Scope window, or enter the data point number in the ‘pnt’ field. X- and Y-measurements are displayed for the cursor pair data points. Fitting can also be applied to the cursor pair data. Right- click on the data, and select ‘Quick Fit’...
Page 353: View Window
4.2.14 3D View Window Show 3D View The Reanalysis Scope 3D View window creates a 3D representation of your data, color-coded to show amplitude variations. Note: If the Igor Pro/SutterPatch main window frame is not wider than the Reanalysis Scope window plus its Analysis sub-window, clicking the 3D button will generate an error mes- sage, but the operation will still execute.
Page 354 Figure 4-80. 3D View A “heat map” bar illustrates the color measurement units. Magnification buttons are located in the upper right corner of the window for the selected axis: All 3 axes. • Sweep Time. • Amplitude. • Time. • DPATCH –...
Page 355 Zoom in Magnify. Zoom out Unmagnify. Autoscale Set to the data limits. X, Y and Z axis limits can be set in the bottom section of the 3D View window. Their delta value is preserved when using the scroll bars to update the visual graph (and the numeric axes limits.) The 3D graph viewing angle can be changed with a set of 3D buttons: = Default View...
Page 356: Routine Review
4.2.15 Routine Review ‘Routine Review’ displays the selected Series data in a modified Reanalysis Scope window defaulted to the ‘Time Course’ display mode. Figure 4-81. Routine Review Open this window from the Data Navigator by highlighting a Series, and selecting the ‘Review Routine’...
Page 357: Routine Settings
New Controls in a signal pane to display the name of the “Series_Signal_Routine”, or on the Click • data to also include the Sweep #, in a field at the bottom of the window. • To reopen a Series from the Routine Review into a Reanalysis scope window, right-click on the Series data, and select ‘Analyze <Routine Name>’...
Page 358 Figure 4-82. Routine Settings Routine Name Displays the Routine name. Activate Opens the Acquisition: Routine Scope window loaded with these settings. Copy to Routine Pool Adds this Routine to the loaded Routine Pool. Routine Description Displays the Routine description. Show Routine Name of the displayed Routine.
Page 359: Single Channel Analysis
Acquisition & Routine Parameters Input Channels Output Channels & Waveform Real Time Measurements & Graphs Preview panel Display of the stimulus waveforms. Copy to Layout Copy the visible stimulus waveforms into a new Layout window, or append to an existing Layout page. Copy to Clipboard Copy the visible stimulus waveforms to the system clipboard.
Page 360 Set Time Range of Analysis Sets the Single Channel Analysis ‘Time Range’ to ‘Sweep Time’, and the ‘Start Time’ and ‘End Time’ are set from the marquee range. Figure 4-83. Single-Channel Scope When single channel analysis is activated, a Single Channel Analysis control panel is opened, and the Reanalysis Scope window active signal is overlaid with the transition levels of the first single- channel opening or closing, based upon the settings in the Single Channel Analysis control panel / Current Transition Controls section.
Page 361 Scope window levels A dashed “Before” line displays the amplitude of the previous transition/event, green  i.e., the level before the transition point. Manually adjust by dragging with the mouse. A dashed “After” line displays the amplitude of the selected transition/event, brown ...
Page 362 Figure 4-84, Single Channel Analysis [ Descriptive Information ] Single Channel Analysis Preferences Dock to scope ------ Baseline Average Duration = x.x ms Calculate the averaged baseline amplitude with the dura- tion of the last baseline data (closed state) before the tran- sition to an open state.
Page 363 Calculate the mean amplitude using up to the duration of the open state data at that level, after a transition to that level. ------ Allow display compression Signal Controls Figure 4-85. Signal Controls Control the display of single channel data in the Scope window. Use individual sweeps Perform analysis on a single sweep at a time.
Page 364 Current Transition Controls Set up the basic level-detection parameters. Figure 4-86. Current Transition Controls Channels open upwards / Channels open downwards Upwards opening channels only accept positive amplitudes. Downwards opening channels only accept negative amplitudes. Amplitude Set to the expected transition size of the initial ion-channel level in the data.
Page 365 Track Limit [ 0 – 1.0 nA ] The maximum (absolute) amount that the Baseline level can change while being automatically tracked. Set manually, or set to 3 * RMS via the ‘Measure RMS’ button. Threshold [ 50 – 90% ] The percentile of the Amplitude value (open state) that needs to be reached by the raw data to “find”...
Page 366 levels might be detected from noise, biological artifacts, or an incorrect initial ‘Start Level’ setting. Status The operational status of the selected transition. Accept Terminates the preceding event and starts a new open/close time. • The selected transition is included in the idealized trace and all Plots.
Page 367 Level 1 openings: The Event duration is from the transition to the Level 1 amplitude, to the next transition to a dif- ferent Level amplitude. Level 2 openings: The Event duration is from the transition to the Level 2 amplitude, to the next transition to a dif- ferent Level amplitude.
Page 368 Single Channels: Plots and Tables Note: All plots and histograms support measuring X-Y data points or setting a fitting range via the ‘Toggle Cursor Info’ right-click menu entry (or Ctrl-I). (See ‘Right-Click Menus’ for Scope windows.) Figure 4-90. Plots and Tables Controls DPATCH –...
Page 369 Current Amplitude Histogram Controls Figure 4-91. Current Amplitude Histogram Controls A current amplitude histogram is often the first analysis performed on an uncharacterized channel, whereby all data points are binned by amplitude. It is used to determine: The quality of the recording. •...
Page 370 To reposition cursors, first create the histogram, and then enable ‘Cursors’ – this will open a Cursor Bar at the bottom of the plot window. Next, drag the cursor’s symbol (labeled “A”, “B”, etc.) from the cursor bar to the new position (near to the X-axis) on the plot.
Page 371 sqrt(y) Use the square-root of the Y-axis data. Open / Closed Select open or closed state data for the Distribution plots. Amplitude Distribution Plot Click to create an amplitude histogram plot of the selected state’s found events. The histogram bin count is reported as ‘Frequency’ on the plot’s Y-axis.
Page 372 Scatter Plot Controls Figure 4-93. Scatter Plot Controls The scatter plot uses “transition deltas” for event amplitudes, which plot on the Y-axis as the directional change in amplitude for each transition; the X-axis plots the duration of the Event. For example, an opening transition to 15 pA will plot on the Y-axis at 15 pA, while a following closing transition back to 0 pA plots on the Y-axis at -15 pA, i.e., the delta of the transition’s Be- fore and After amplitudes.
Page 373 Table Controls Figure 4-94. Table Controls Table of Transitions Click for a listing of all transitions. Layout of the table Top Row: [ Cell address | Cell value ] Column Number Row: Column numbers [ 0, 1, 2, … ] Row 0: Status The operational status of the selected transition.
Page 374 Row 4: Amplitude_After Amplitude of the transition, i.e., the level after the transi- tion point. Row 5: Duration Duration of the transition. Note: The last column of transition data is preset to a zero duration. Row 6: Amplitude Amplitude of the transition. Row 7: Amplitude_Valid Include / Exclude the transition for processing.
Page 375 Table Column Labels Gaussian Fit Header Row Row 0 Source Sweep_# Analysis Current Amplitude Histogram Fit, or Amplitude Distribution Fit Label1 Amplitude Value1 Label2 p(closed) Value2 Label3 p(open) Value3 Label4 Gauss_y0_1 Value4 Label5 Gauss_A_1 Value5 Label6 Gauss_x0_1 Value6 Label7 Gauss_width_1 Value7 Label8 Success_1...
Page 376 Label15 Gauss_A_3 Value15 Label16 Gauss_x0_3 Value16 Label17 Gauss_width_3 Value17 Label18 Success_3 Value18 Linear Exponential Fit Header Row Row 0 Source Sweep_# Analysis Duration Distribution Fit Label1 Exp_y0 Value1 Label2 Exp_A Value2 Label3 Exp_Tau Value3 Label4 Exp_0 Value4 Label5 Success Value5 Logarithmic Exponential Fit Header Row Row 0...
Page 377 Value4 Label5 Success Value5 DPATCH – OPERATION MANUAL – REV. 2.3 (2022-10-24)
Page 378: Synaptic Event Analysis
4.2.18 Synaptic Event Analysis SutterPatch: Available Analysis Modules: Synaptic Event Analysis Post-synaptic potentials and currents from excitatory and inhibitory events (EPSPs, EPSCs, IP- SPs, IPSCs) are analyzed with this application module. Access via the Reanalysis Scope window ‘Measurements’ button or the Data Navigator (signal) ‘Available actions’ menu. Spontaneous miniature events (mEPSPs, etc.), which generate small and often overlapping Events, are detected with an innovative deconvolution algorithm.
Page 379 Sweep # The sweep number of the displayed data. The Sweep # is set to ‘0’ when the Average event is displayed in the Event pane (or when the template is initially created prior to analysis.) Select arbitrary sweeps for processing by “marking” them in the Data Navigator tree, or in a Scope window during acquisition or reanalysis.
Page 380 Realign average Allow realignment of the ‘Use average’ template to keep the anal- ysis from drifting Detection Menu Open the Levels sub-panel to configure detection levels. Threshold (xSD) A detection threshold represents the “Event Strength”. A lower (“weaker”) number finds more events, while a higher (“stronger”) number finds less events.
Page 381 mouse marquee tool, and right-click for the marquee menu. The special menu option ‘Add Mini’ allows you to manually classify a raw data selection as an event during manual detection, or to include an event missed by the template detection. The new event is highlighted in red, and included in new Results tables.
Page 382 Note: The individual graphs are also ac- cessible via Windows / Graphs. Results Table A table of columns is created. [ blank ] Row number with one row per Event. Sweep Number The sweep number the Event is in. Event Time (s) ‘Time to event’...
Page 383: Command Window
4.3 General SutterPatch general operations. Note: Hidden unminimized windows can be brought into view with the menu command Win- dows / Control / Retrieve All Windows. 4.3.1 Command Window Windows: Command Window This window is an Igor Pro code interpreter, and provides programmatic interaction with SutterPatch.
Page 384: Dashboard Panel
Show event tags in reanalysis scope: ON/OFF Number format: (for table export) The lower section is a command buffer with a “command line”, where commands to be executed are entered. Commands can be placed into the command buffer in multiple ways: Manually type (or copy and paste) a line of text into the command line.
Page 385 Settings Dashboard Settings menu. Large Display key areas as large icons in a Dashboard pane. Vertical When the Dashboard ‘Acquire Data’ sub-pane is open, dock it below the main Dashboard pane. Horizontal When the Dashboard ‘Acquire Data’ sub-pane is open, dock it on the right-side of the main Dashboard pane.
Page 386 View Last Data Open the Experiment’s last recorded data Series. All sweeps (marked and unmarked) are visible in the initial display. Set Metadata Configure metadata settings and values. New Experiment Start a new Experiment, and/or switch the amplifier model or emulation mode. Note: During the shutdown of the existing Experiment, it is highly recommended to say “Yes”...
Page 387: Figure 4-97. Dashboard - Acquisition
Figure 4-98. Dashboard - Acquisition Control Panel Hardware control via the Amplifier Control Panel. Membrane Test Monitor seal formation and cell health. Free Run Run an oscilloscope-style signal monitor. Routines Configure Routine acquisition settings. Paradigms Control the execution of Paradigm commands. Small Icons Display the SutterPatch dashboard as small icons in a floating toolbar.
Page 388: Figure 3-9. Dynamic Clamp Editor
Icon Icon Name Shortcut Key Acquisition Control Ctrl-0 Scope Window Ctrl-2 Amplifier Control Panel Ctrl-3 Membrane Test Ctrl-4 Free Run (Scope) Ctrl-5 Paradigm Editor Ctrl-6 Routine Editor Ctrl-7 Dynamic Clamp Editor Template Editor Equation Editor Solution Editor Camera Control Data Navigator Ctrl-8 Analysis Editor Layout Page...
Page 389: Documentation
Notebook Shortcut Editor View Last FN-F2 New HDF5 File / New Experiment 4.3.3 Documentation Help Help: Help Topics Full online Help for the SutterPatch software and all models of Sutter Amplifier Sys- tems is available via Igor Pro’s ‘Help Browser’. In the browser’s ‘Help Topics’...
Page 390: File Types
macOS: In the PDF document, click the ‘Contents’ button on the left side of the PDF Navigation Toolbar, or the ‘Page Thumbnails’ button left of the sidebar, and select ‘Table of Contents’. QuickStart Guide A printed “quick” installation guide for your Sutter hardware and software. Important! Contains your Igor Pro 9 Serial Number and Registration Key.
Page 391 Much more disk space is used, especially for Experiments that have a lot • of small waves. The UXP format is more “fragile”, as you need to keep the Experiment • file and its corresponding folder together when you copy or move the Ex- periment.
Page 392: Layout Window
Igor Pro Files Data can be selected and exported to the Igor Pro file format (*.ibw) via the Data Navi- gator ‘Available Actions’ menu. Select the Igor Binary format in SutterPatch / Set Pref- erences / Data Export. Igor Pro binary waves (*.ibw) can be loaded into the current Experiment via Data / Load Waves / Load Igor Binary.
Page 393 exists at a time. If no Layout window exists, it can be manually created via the ‘Layout’ button located in various windows. The Layout window can also be created by running a Paradigm ‘Export’ step. Note: Layout windows are sometimes created hidden behind other windows. Clicking a Layout button appends its associated items into an existing Layout page (or a new Layout window.) Each signal and analysis graph is appended as an individual object.
Page 394: Log Window
4.3.6 Log Window SutterPatch: Log Window The Log window displays time-stamped commands, responses, administrative information and error messages that provide a history of the steps having a possible influence on the execution of the experiment and its data. The Log window can also serve as a user laboratory notebook for free-form entries.
Page 395: Menus
Each row with a Data Acquisition, Metadata or Paradigm entry is appended with the name of the appropriate Routine or Paradigm; if there is no value to list, just the name of the Routine or Paradigm is displayed. 4.3.7 Menus The SutterPatch main menu item contains all of the SutterPatch-specific menu items.
Page 396 If no active hardware is attached, the original amplifier configuration of the Experiment will be automatically used for the SutterPatch demo mode. If the SutterPatch preference for HDF5 files was enabled, a “SutterPatch Question” will ask how to load the matching HDF5 file: Load matching HDF5 File: [ pathname ] Load in modify mode, i.e., add new data, store...
Page 397 If Preferences are enabled for automatic file naming, an incrementing Experiment name is displayed for renaming and saving. However, nothing else in the Experiment gets saved. -------------------- Recent Experiments A list of recently used Experiments. Exit An Experiment file ‘Save’ dialog is displayed before clos- ing the program.
Page 398 Windows The Windows menu provides access to all window controls. Command Window A quick code interpreter to manually process SutterPatch and Igor Pro commands. Control / Retrieve All Windows Hidden unminimized windows can be brought into view with the menu command. Layout The Layout menu only displays when a Layout is the active window.
Page 399 Routine Editor Open a window to load and edit Routines. Dynamic Clamp Editor Open a window to edit and load Conductance models. Template Editor Open a window to manage templates. Equation Editor Open a window to load and edit Equations. Solution Control Open a window to control solutions.
Page 400 Action Potential Analysis Synaptic Event Analysis Single Channel Analysis Help Igor Help Browser Igor Pro and SutterPatch Help Topics. About SutterPatch SutterPatch version and contact information. Scope Right-click Menus Different areas of the Scope windows support additional functionality through "right-click" menus in Windows, or "Command-click"...
Page 401 Autoscale All Axes • Add Annotation • Export Graphics Copy the selected signal to a Graph window. • Toggle Cursor Info Manually measure X-Y data values or set a fitting • range. Colors • Hide Signal ‘<signal name>’ • Show Signal ‘<signal name>’ Only •...
Page 402 Hide Sweep_# • Duplicate Sweep_# • Replace Wave • Copy • Modify Sweep_# • Customize at Point • Mode • Line Style • Line Size • Markers • Marker Size • Color • Bring to Front • Send to Back •...
Page 403: Notebook
Vert Shrink • ---------------------- Extract Template • 4.3.8 Notebook SutterPatch: Notebook The SutterPatch Notebook is a free-form text-entry lab Notebook, that also receives Igor Pro cursor measurements, and optional system logging information. Figure 4-100. Notebook Clear Clear the complete Notebook content. Copy to Layout Click to copy the selected text or the compete (unselected) Note- book into a new Layout window, or to an existing Layout page, as...
Page 404: Sample Files
4.3.9 Sample Files Sample settings files (subject to change) are included in the .. / Documents / SutterPatch / Pa- rameters folder: Compound Pool SP_CompoundPool.spl 1. undefined No compounds are configured. Dynamic Clamp Pools SP_DynamicClampPool.spd [ for dPatch systems ] 1.
Page 405 Paradigm Pools LockIn / LockIn_dPatch.spp [ for dPatch systems ] 1. LockIn_Adjust_500Hz 2. LockIn _ Adjust_1kHz 3. LockIn _ Adjust_2kHz 4. LockIn _ Adjust_5kHz 5. LockIn _ Adjust_10kHz 6. LockIn _ Adjust_20kHz 7. LockIn _DoAdjust LockIn / LockIn_IPA.spp [ for D/IPA systems ] SP_ParadigmPool_Dendrite.spp [ for Dendrite systems ] SP_ParadigmPool_dPatch.spp...
Page 406 Routine Pools LockIn / LockIn_DIPA.spr [ for Double IPA systems ] LockIn / LockIn_dPatch.spr [ for dPatch systems ] 1. phase delay 2. LockIn _500Hz 3. LockIn _1kHz 4. LockIn _2kHz 5. LockIn _5kHz 6. LockIn _10kHz 7. LockIn _20kHz LockIn / LockIn_IPA.spr [ for IPA lock-in tuning ] SP_RoutinePool.spr...
Page 407 14. Recovery_SlowInact Recovery from slow inactivation. 15. SS_SlowInactivation Steady-state slow activation. 16. Synaptic_Stim Synaptic stimulation. 17. Synaptic_Stim30 Synaptic stimulation for 30 s. 18. Synaptic_StimPlusDig Synaptic stimulation with digital output. 19. Template_PlusVirtual Template wave and recording virtual signals. 20. Template_SpontAct Template wave from a recorded signal. 21.
Page 408 Shortcut Pool SP_ShortcutPool.sps 1. VHold + 10mV Increase the Control Panel V-holding level by 10 2. VHold – 10mV Decrease the Control Panel V-holding level by 10 3. VHold + 1mV Increase the Control Panel V-holding level by 1 4. VHold – 1mV Decrease the Control Panel V-holding level by 1 5.
Page 409: Set Metadata
3. HodgkinHuxley 4. Noise Experiments Sample data (subject to change) are included in the ... / Documents / SutterPatch / Example folder: ActionPotentials.pxp Action potential data. LargeAPs.pxp Large action potentials data. MiniExample.pxp Spontaneous miniature synaptic potential data. 4.3.10 Set Metadata SutterPatch: Set Metadata A variety of optional experimental parameters (preparation, electrode, etc.) can be associated with an Experiment, Paradigm, or Routine as user-configurable “metadata”.
Page 410 Show Summary An overview of the user-defined metadata parameters. Metadata Summary dialog This list summarizes all Metadata parameters (from all Metadata detail levels) for which values have been defined. Double-click a line to show and edit the details for a parameter. Metadata Parameter Parameter name.
Page 411 Configuration choices for the selected parameter Note: Values in this dialog are updated by acquisition changes after the dialog is closed and re-opened. Do not write this parameter This parameter is not stored. • If this parameter was previously written in this Experiment, then its Previous Value is displayed.
Page 412 Write Enable to write the selected metadata parameter with the Experiment, Paradigm or Routine. Metadata Parameter The name of the selected metadata parameter. Next Value The metadata value to write. Update Enable so that edits made to ‘Value’ will update the ‘last value’ for the next prompt.
Page 413 BASIC EXTENDED FULL GROUP / Parameters Notes OPERATOR Full Operator Name PREPARATION - ANIMAL Animal Identifier Animal Species Binomial species name Strain, breed or variety Animal Strain characterizing the animal Animal Genotype Animal Age Animal Age Unit Ex.: h, d, m Ex.: 1: F, 2: M, 3: Undeter- Animal Sex / Gender mined...
Page 414 Tissue User Parameter 3 Name Tissue User Parameter 3 Tissue User Parameter 4 Name Tissue User Parameter 4 Tissue User Parameter 5 Name Tissue User Parameter 5 PREPARATION - CELL Cell Preparation Identifier Acutely Dissociated Cells Cell Line Slice Preparation Whole-organ Preparation In-situ Recording Stem Cell Preparation...
Page 415 Experiment Category 1 Experiment Category 2 Name Experiment Category 2 Experiment Category 3 Name Experiment Category 3 Experiment Category 4 Name Experiment Category 4 Experiment Category 5 Name Experiment Category 5 Experiment User Parameter 1 Name Experiment User Parameter 1 Experiment User Parameter 2 Name Experiment User Parameter 2 Experiment User Parameter 3 Name...
Page 416 Electrode Coated Electrode Coating Material Electrode Beveled Electrode Bevel Angle Electrode User Parameter 1 Name Electrode User Parameter 1 Electrode User Parameter 2 Name Electrode User Parameter 2 Electrode User Parameter 3 Name Electrode User Parameter 3 Electrode User Parameter 4 Name Electrode User Parameter 4 Electrode User Parameter 5 Name Electrode User Parameter 5...
Page 417 Solution User Parameter 2 Name Solution User Parameter 2 Solution User Parameter 3 Name Solution User Parameter 3 Solution User Parameter 4 Name Solution User Parameter 4 Solution User Parameter 5 Name Solution User Parameter 5 PARADIGM Bath Temperature Bath Temperature Unit Ambient Temperature Ambient Temperature Unit Atmospheric Composition...
Page 418 STIMULUS Key Stimulus Stimulus Duration Stimulus Control Signal Compound Group Compound Group Index Compound Identifier Compound Name Compound Description Compound Concentration Compound Concentration Unit Compound Batch Compound Lot Compound Preparation Date Compound Preparation Time Compound Salt Code Compound Source Compound Solution Compound Vehicle / Solubility Enhancer Compound Vehicle Concentration Compound Vehicle Concentration Unit...
Page 419 Light Stimulus User Parameter 3 Name Light Stimulus User Parameter 3 Light Stimulus User Parameter 4 Name Light Stimulus User Parameter 4 Light Stimulus User Parameter 5 Name Light Stimulus User Parameter 5 Mechanical Stimulus Intensity Mechanical Stimulus Intensity Unit Mechanical Stimulus User Parameter 1 Name Mechanical Stimulus User Parameter 1...
Page 420: Set Preferences
Thermal Stimulus User Parameter 4 Thermal Stimulus User Parameter 5 Name Thermal Stimulus User Parameter 5 The frequency of an exter- Electrical Stimulus Frequency nal electrical stimulus The intensity of an exter- Electrical Stimulus Intensity nal electrical stimulus The intensity unit of an Electrical Stimulus Intensity Unit external electrical stimu- Electrical Stimulus User Parameter 1 Name...
Page 421: General
Figure 4-102. Preferences Settings General Don’t wait at Startup Panel Skip the “Welcome” screen during startup and directly launch SutterPatch with a new Experiment. The options to startup just ‘Igor Pro’, or to re-open a saved Experiment, are bypassed. Show preferences summary on startup Display the ‘Summary of Major Preferences’...
Page 422 Warn when file size exceeds limit of 500 MB|OFF Maximal sweeps displayed in persistence display during acquisition: # | all Maximal sweeps displayed in persistence display during reanalysis: # | all Show event tags in reanalysis scope: ON|OFF Number format: Use exponential | engineering and also display this summary in the startup Command window.
Page 423: Files And Naming
Note: You can also bring all unminimized windows into view with the Windows > Control > Retrieve All Windows menu command. Feedback notice display duration [ 1 – 30 s ] Control how long SutterPatch messages display for reading, before automatically closing. Preferences Defaults Restore default settings for all preferences.
Page 424 delays when saving experiments. Default file paths Windows: C:\Users\<User Account Name>\Docu- ments\SutterPatch\Data\ macOS: Applications/ SutterPatch2/SutterPatch/Data/ Enable automatic naming for experiment Experiment file name example: (Maximum 34 characters) At least one of the following file name components must be enabled: Text: Include user text at the start of the file name.
Page 425 started a "New Experiment", but without starting a new SutterPatch session. The raw signal data are stored to the HDF5 disk file during acquisition after each sweep, instead of storing all data at the end of an Experiment, which can be a time-consuming experience.
Page 426 The non-data information are automatically written to the HDF5 file at the end of an Experiment. However, if this option is enabled, the information is also auto- matically written to the HDF5 file at the end of each Series. Compact HDF5 file on closing [ only displays when “Save data to HDF5”...
Page 427: Hardware
delays after a recording is stopped. This provides the fastest method of operation when making multiple recordings, but is also the least secure, as data loss can occur if the computer encounters problems. Warn when file size exceeds limit When a recording causes the Experiment to exceed the desired limit, a notification message displays after the Routine stops.
Page 428: Control Panel
Voltage Clamp and Current Clamp modes. If you are routinely losing cells when switching into Current Clamp mode, increase this setting from the default ‘0.5’ to ‘1’ or ‘2’. Note: The electrode compensation reduction is done in the back- ground, and does not affect the Control Panel current-clamp settings.
Page 429: Scope Window
Scope Window Scope setting changes are applied to an acquisition Scope window at the time of window creation, and to a reanalysis.Scope window when data is loaded. General Time axis unit: Auto-set Sweep duration < 120 s, use “s” • Sweep duration >= 120 s, use “min”...
Page 430 Reanalysis Persistence Keep current setting Maximal sweeps displayed in persistence display [ 2 – 100 ] (30 = default value) The last ‘N’ sweeps are displayed [ All ] All sweeps are displayed. Improve data readability by restricting the number of sweeps displayed. This can also improve system performance by reducing the display processing load.
Page 431 System • Tag text box Relative Time Time from beginning of Series. • [ hours to milliseconds ] Absolute Time Clock time. • [ hours to milliseconds ] Description User Comment, from ‘Set Tag’. • Tag appearance Color by type •...
Page 432: Metadata
Metadata Metadata setup detail level: Select level for metadata setup categorization complexity. Select which metadata groups and parameters are visible for setup in ‘Set Metadata’ and Data Navigator / ‘Build Hierarchy’. Basic Show only the most essential parameters. Extended Show additional detail. Full Expose all available metadata parameters.
Page 433 • • 2 x 2 (Column x Row) • 2 x 3 (Column x Row) • 2 x 4 (Column x Row) • Graphs left (the Y-axis) Tick location: Outside • Crossing • Inside • None • Labels: • Axis only Text labels only.
Page 434: Data Export
Axis only Text labels only. • • Grid: • • Major only • viii. Data Export File Export • Igor Binary Format Save the signal formatted as an “Igor Binary Wave” file (*.ibw). Export all selected sweeps to one file per signal (one 2D wave) •...
Page 435: Factory Reset
• <CR> (Igor Pro, macos) • <CR> <LF> (Windows) Invalid value Use NaN • Use empty string • Use zero • Digits in table entries [ 3 – 15 ] Use Scientific format Use exponential notation (e.g., 10e-3 V) • Use engineering prefix (e.g., mV) •...
Page 436: Shortcut Editor
4.3.12 Shortcut Editor SutterPatch: Shortcuts: Shortcut Editor Keyboard control of SutterPatch is available by configuring keyboard shortcuts. Figure 4-103. Shortcut Editor All assigned Control (Command), Function and Shortcut Action key combinations are automat- ically added to the main menu SutterPatch / Shortcuts submenu. All Control and Function Key Assignments are automatically saved when the program is closed.
Page 437 Windows: Control key: Ctrl • macOS: Command key: • and clicking its assigned number key. Control keys and their default SutterPatch menu assignments: Control-1 Dashboard Control-2 Scope Window [ Scope window must be open. ] Control-3 Amplifier Control Panel Control-4 Membrane Test Control-5 Free Run (Scope)
Page 438 Note: On some keyboards, you also need to press the ‘Fn’ key to use Function keys. Also, macOS reserves nearly all Function keys for itself. In order to use Func- tion keys for a macOS application, you must first check a checkbox in the ma- cOS Keyboard control panel.
Page 439 Save Shortcut Pool As… Save the Shortcut Pool to a new file, and switch to the new file. The default file name is the same as the original file name. Save Shortcut Pool Copy… Save the Shortcut Pool to a new file, but do not switch to the new file.
Page 440 Predefined Shortcut Actions [Hold+10mV|10 pA: Right] (keyboard arrow key) [Hold-10mV|10 pA: Left] (keyboard arrow key) [Hold+1mV|1 pA: Right, shift] (keyboard arrow key) [Hold-1mV|1 pA: Left, shift] (keyboard arrow key) [View last] [Stop Acquisition] [Start Routine] [Stop Routine] [Pause Paradigm] [Resume Paradigm] [Cursor Info] [Next Sweep]] In Reanalysis Scope.
Page 441 Select Series Display the next/previous series in the Reanalysis Scope window. Select Sweep Set a sweep to be the “active” sweep. Set Axis Modify the axis scaling of a signal. Set Checkbox Set local and global checkboxes for conditional processing in Paradigm ‘If’...
Page 442: Sutterpatch Startup
4.3.13 SutterPatch Startup The SutterPatch application startup sequence: Power-on the dPatch amplifier by pressing the silver POWER button on its front – it lights up as blue. (It can take a few seconds for the USB connection to be established Click on the ‘Igor Pro 9’...
Page 443 Selected amplifier: dPatch Automatic experiment naming is ON: <pathname> Save data to separate HDF5 file is OFF Save entire experiment after each routine Warn when file size exceeds limit of 500 MB Maximal sweeps displayed in persistence display during acquisition: 30 Maximal sweeps displayed in persistence display during reanalysis: 30 Show event tags in reanalysis scope: ON Number format: Use exponential notation (e.g., 10e-3 V)
Page 444: Programming
5. PROGRAMMING 5.1 Data Format SutterPatch data are written in a 64-bit double-precision binary floating-point format. This supports a decimal precision of 17 significant digits. The data are stored within an Igor Pro Experiment (*.pxp) file. For large data sets, an optional HDF5 file format will be available for streaming data acquisi- tion without resaving the experiment at the end of a recording.
Page 445 #pragma TextEncoding = “Windows-1252” #pragma rtGlobals=3 // Use modern global access method… #include “SP_Globals”, optional Function SayHello() DoAlert 0, “Hello World!” Note: The Function name must include trailing open/close parentheses “( )”. 3. Click on the Compile button at the bottom of the window. 4.
Page 446: Troubleshooting
(+1) 415.883.0572 info@sutter.com E-mail: Address: Sutter Instrument Company One Digital Drive Novato, CA 94949 When contacting us for technical support, please provide your SutterPatch version and “build” num- bers to help us troubleshoot your situation. These numbers are found in the Start splash screen dur- ing program loading, or in the Log Window Startup events.
Page 447: Startup Issues
Some SutterPatch error messages or notifications will flash to get your attention, and automatically close after several seconds, and then write to a “History” window. To review such messages, see the Command window (menu item Windows / Command Window). 6.4 Startup Issues 6.4.1 Installation Fails Problem:...
Page 448 Units will not power up with a fully discharged battery. In this case, request a replacement firmware board with non-volatile memory from Sutter Instrument Current dPatch systems use non-volatile memory, which does not use a battery.
Page 449: Acquisition Issues
6.4.6 USB Communication Fails Problem: When starting up SutterPatch in Windows, there is no USB communication with the computer. Solution: Power off the amplifier, then reseat the USB cable on both ends, and then power on the amplifier. Or, the Windows “power plan” might have disabled the USB ports. 1) Go to the Windows Start screen, and enter “edit power plan”...
Page 450 Problem: Selecting a Routine in the Routine Editor suspends the SutterPatch program. Solution: Hide the Routine Editor Preview pane. If there is a very large number of sweeps to display, the Preview pane can take a long time to redraw, and the program becomes temporarily unresponsive. 6.5.2 Routine Pre-Loading Delays Problem:...
Page 451 6.5.6 Acquisition Windows Lock Up Problem: The Scope window, Routine Editor or Paradigm Editor lock up during acquisi- tion. Solution: Use the menu command SutterPatch / Reset Acquisition to halt acquisition. A combination of SutterPatch-related and computer-related issues can contrib- ute to your system’s performance.
Page 452 6.5.11 Paradigm Sound Reduced Problem: The paradigm ‘Sound’ step volume is attenuated at lower frequencies. Solution: Upgrade the computer speaker, such as with add-on speakers. 6.5.12 Offset Zero Delay Problem: The Offset button in the IPA Control Panel has a short delay before it responds. Solution: This can occur after running the Membrane Test due to internal processing.
Page 453 Upgrade: Computer graphics card. Increase: Computer RAM, cache size and/or CPU speed. 6.5.15 Heavy Duty Acquisition (& Analysis) Problem: MHz acquisition puts the CPU performance, memory requirements and disk speed under stress. Acquiring one channel for 1 minute at 5 MHz will create a sweep which is 2.4 GB in size, a very large data block.
Page 454 Check: CPU is a dual-core processor (i5) or higher. This is a base requirement for SutterPatch. Use: Igor Pro 9. This version is much more responsive than Igor Pro 8 during ac- quisition. Routines Hide: Routine Editor Preview pane If there is a very large number of sweeps to display, the Preview pane updates can take a long time to redraw, and the program becomes temporarily unresponsive.
Page 455: Analysis Issues
6.5.16 USB Errors Problem: A USB communications error occurs. Solution: Right-click in the amplifier Control Panel and select Reset USB . If the USB button does not turn from red to green, then try to isolate the problem. a) Unplug and re-plug both ends of the USB cable from the amplifier to the computer.
Page 456: General Issues
displayed. Switch to a tiled signal layout, or reduce the number of visible sig- nals by right-clicking a signal and selecting ‘Hide Signal’. Graphs & Layouts Not Visible 6.6.3 Problem: Cannot see SutterPatch Experiment graphs or layouts on non-SutterPatch com- puters.
Page 457 6.7.4 Slow Window Opening/Closing Problem: Window opening and closing is slow on the macOS. Solution: Close the SutterPatch Data Browser. This function consumes a lot of system resources. 6.7.5 Windows Slowly Move Up or Down the Screen Problem: Various SutterPatch windows in the Windows OS slowly creep up or down the screen, until they get to the top or bottom frame of the SutterPatch main win- dow.
Page 458 Solution: This can occur on high-resolution monitors running on older versions of Win- dows 10. Upgrade to the current version of Windows 10. 6.7.10 Magnification Corrupts Window Problem: After applying right-click Expansion to a window, returning to normal magnifi- cation corrupts the window. Solution: Disable the Set Preferences / General / ‘Automatic window repositioning’.
Page 459: Appendix A: Limited Warranty
Warranty work will be performed only at the factory.  The cost of shipment both ways is paid for by Sutter Instrument Company during the first three  months this warranty is in effect, after which the cost is the responsibility of the customer.
Page 460: Appendix B: Software License
Agreement. Section 1.2. “Confidential information” means any data or information, oral or written, of Sutter Instrument Corp., including without limitation, past, present, or future re- search, development or business activities, including any unannounced product(s) and...
Page 461: Grant Of License
Section 2.1. Evaluation License. If the Product is used for evaluation, trial or demon- stration purposes, Sutter Instrument Corp. grants such user a license solely for the pur- pose of evaluating, sampling, testing, or demonstrating the Product for the timeframe specified in the evaluation period.
Page 462 ownership interest whatsoever in the Product by its use of the Product, which ownership rights shall reside solely with Licensor or its affiliated companies. Section 3.3. Licensee acknowledges and agrees that Licensee (and Licensee’s End Users) is solely and exclusively responsible for contents, data, information and communications that the Licensee and End Users upload and transmit through the Website to use the Product.
Page 463 valid and correct tax exemption certificate prior to order acceptance. The payment of such tax is the sole responsibility of Licensee. 5. SUPPORT. Section 5.1. Licensor shall provide Licensee with a technical help desk facility to report prob- lems or questions relating to the Product. The help desk is available by email at the following ad- dress: info@sutter.com, or by calling the Licensor at 415-883-0128 between 8:00am and 5:00pm, Monday through Friday, Pacific Time.
Page 464: General Provisions
Licensee agrees to refrain from disclosing the Product software (and to take reasonable measures with its employees to ensure they do not disclose the Software) to any person, firm or entity except as expressly permitted herein. 8. TERMINATION. Section 8.1 This Agreement shall become effective upon the use of the Product.
Page 465 Section 10.2. This Agreement constitutes the entire understanding and agreement between Li- censor and Licensee regarding its subject matter, and supersedes all previous oral and written communications, agreements, memoranda, representations, or understandings between Licensor and Licensee regarding this Agreement. No other rights or licenses are granted to Licensee, ex- cept as expressly provided herein.
Page 466 Section 10.11. Any amendments or addenda to this Agreement, may be executed in counter- parts, each of which will be considered an original, but all counterparts together will constitute one agreement. A facsimile of a signed copy of this Agreement, or an electronic or other digital signature imprinted on this Agreement, may be relied upon as an original.
Page 467: Appendix C: Accessories
APPENDIX C: Accessories dPatch Expansion Panel Rack-mountable analog and digital I/O BNC panel. • Ground Point Grounding point hardware. • DPATCH-PCH dPatch Expansion Panel This optional rack-mountable panel provides BNC ports for easy access to all dPatch digital I/O channels and rear-panel auxiliary analog channels. Figure C-0-1.
Page 468: Figure C-0-2. Ground Point
GP-17 Ground Point For system grounding, this optional machined brass tower provides reliable low-resistance con- nections for electrophysiology setups. The base plate mounts directly to air table tops (imperial and metric) with the included ¼-20 and M6 screws. The plated connectors accept up to 9 ba- nana plugs and 8 bare wires (up to 10 gauge).
Page 469: Appendix D: Fuse Replacement
APPENDIX D: Fuse Replacement In the event that the instrument fails to power up when it is switched on, the power-line fuses should be checked to determine whether they have blown. Two fuses are located in the fuse holder in the power cord module on the rear of the amplifier. To replace a fuse: 1.
Page 470: Appendix E. Technical Specifications
APPENDIX E. Technical Speci fications General Specifications dPatch Amplifier – Physical Dimensions (in.) (includes handles 19 (W) x 11 (D) x 3.5 (H) & connectors) Dimensions (cm) (includes handles 48.2 (W) x 28 (D) x 9 (H) & connectors) Weight (lb) (with headstages) Weight (kg) (with headstages)
Page 471 DEFINITION Digital Output 1 Digital Output 2 Digital Output 3 Digital Output 4 Digital Output 5 Digital Output 6 Digital Output 7 Digital Output 8 Digital Output 9 Digital Output 10 Digital Output 11 Digital Output 12 Digital Output 13 Digital Output 14 Digital Output 15 Digital Output 16...
Page 472: Table E-1. Dpatch Amplifier - Physical
+5 V +5 V Pin numbering Right to left, top to bottom. Table E-1. dPatch Amplifier - Physical dPatch Headstage - Physical Construction Anodized aluminum case Dimensions (in) 3.7 x 1.1 x 0.66 [ L x W x H ] Dimensions (cm) 9.5 x 2.9 x 1.7 [ L x W x H ]...
Page 473: Table E-3. Dpatch Headstage - Operational
(Measured with 8-pole Bessel filter.) Series Whole-cell Electrode Amplitude Resistance Capacitance Feedback Analog Compen- Range Compensation Compensation Element Bandwidth sation Range Range Range 1 pF Ca- ± 20 nA 0.0 - 20 pF > 500 kHz pacitor 500 MΩ 0.0 - 20 pF >...
Page 474: Table E-5. Dpatch Headstage - Grounded Input Noise
50 MΩ 1 µV 700 nV 400 nV Resistor Table E-5. dPatch Headstage – Grounded Input Noise dPatch Headstage Inputs – Risetime (CC) (Measured with ±20 nA range.) Series Resistance Rs Pipette Capaci- 10-90% Risetime Bandwidth tance 0 Ω 10 pF 250 ns 1.4 MHz 100 kΩ...
Page 475 Auxiliary I/O Channel 16 bits Resolution Auxiliary In Sample Rate 200 kHz Auxiliary In Bandwidth 1 - 200 kHz Auxiliary Out Sample 250 kHz Rate Auxiliary Out Current 20 mA (max) 0 -0.8 V = Low Digital In States 2.0 – 5.5 V = High 0 –...
Page 476 The included Screw Terminal Board attaches to the dPatch rear panel DIGITAL OUTPUTS connector. Digital output signal wires need to be manually screwed into the appropriate pin number. An inter- vening 37-pin cable (not included) can also be used to extend the length of the Screw Terminal Board. dPatch Electrical Power consumption 18 Watts maximum...
Page 477 Silver Wire • Body/Barrel (standard: quartz; optional: polycarbonate) • Wire Seal (tubing) • Gold Pin • Pin Cap • Lockdown Ring • Barrel + Tubing Suction Tube Lockdown Ring + Pin Cap End Cap + Gasket Silver Wire Gold Pin 1.597”...
Page 478: Action Potential Threshold Algorithm
APPENDIX F. SutterPatch Algorithms Action Potential Threshold Algorithm [ for Action Potential Analysis ] Results pane ‘Threshold potential’ computation: The Event starts when the signal slope is > 1 mV/100 µs (10 V/s), or when 25% of the maximum slope is reached, whichever is smaller. The exact ‘Threshold potential’...
Page 479: Auto 'Electrode Compensation' Algorithm
Integral from latency (i.e., pipeline samples plus stimulus-filter delay) over a time range of 4 * half-decay time. These first estimates are iteratively improved by the method as described by Sigworth et al (1995), J Neurosci. Methods, 56:195-202. Iterations are terminated when the improvements get less than 2%, or after 10 iterations. Notes: Estimating Rs by Rs = tau * dV / Qt (as used in the membrane test), underestimates Rs •...
Page 480: Auto Offset Algorithm
“CurrentGain" is the gain of the dPatch current input, 50 MΩ or 5 MΩ, as de- fined by feedback mode (or 50e6 V/A and 5e6 V/A, since an Ohm is defined as 1 V/A.) The computed capacitance value is used as a correction value that is added to the electrode ca- pacitance magnitude.
Page 481 [ for the Amplifier Control Panel ‘Liquid junction’ correction ] Bath Offsets Command Offsets When a micropipette is placed into the bath, a voltage-clamp “zero-volt” stimulus command can still generate a small amount of unwanted current flow. Correspondingly, a current-clamp “zero-current” stimulus command can generate a small amount of unwanted voltage charge.
Page 482 Inside of Cell → Outside of Cell | Bath (0 V) (Positive Polarity) → Membrane Potential Membrane potential (V ) is defined as: – V Voltage on the cell inner membrane. Voltage on the cell outer membrane. As in the bath, then –...
Page 483 IV Patch Configurations Voltage Levels In a patch-clamp experiment, baseline voltage levels change (pre- vs. post-seal) by the magnitude of the liquid junction offset. However, the polarity of the LJP correction is handled differently for the various patch configurations. “Outside-Out” Configurations Outside of cell membrane: in bath Inside of cell membrane:...
Page 484 conventional cell membrane measurements. So, to “add” an LJP value into a membrane equation, you actually subtract it. The Membrane voltage equals the Command voltage “minus” the LJP. For whole-cell Current Clamp mode, where “V is the measured voltage from rec”...
Page 485 “Outward” currents flow from the inner to outer membrane, so these • currents flow into the micropipette with a negative polarity. These “inside-out” patch configurations utilize reversed polarity from “conventional” cell membrane polarity: Inside-Out This configuration is useful for studying single channel activity, while modifying the internal milieu.
Page 486: Lockin Computation
LockIn Computation [ for Routine Editor Virtual Input Channels ] LockIn paper: Lindau, M., Neher, E. Patch-clamp techniques for time-resolved capacitance measure- ments in single cells. Pflugers Arch. 411, 137–146 (1988). https://doi.org/10.1007/BF00582306 Math used in the LockIn computation: Factor = ( 2.0 / SinePointsPerCycle ) / sine_amplitude^2 A = Factor * ∑( current * stim_real ) ∑...
Page 487 The following parameters are calculated: Exponential curve fitting Transient peak amplitude (It) Fitted curve time constant (τ or tau) Electrode access resistance (Ra) Membrane resistance (Rm) Steady-state response (I1, I2) Steady-state current (Iss) Charge (Q) Membrane capacitance (Cm) Stimulus The stimulus is a square-pulse wave, i.e., each pulse width is 50% of the pulse period (cycle), with the peak-to-peak amplitude centered around the cell’s rest- ing potential.
Page 488: Figure 0-1. Mt Command Pulse & Response
Steady-State Response Figure 0-1. MT Command Pulse & Response A square-pulse stimulation generates a pair of equal duration amplitude levels. The pulse level amplitudes (V1, V2) should be centered around the cell’s resting potential. Note: The SutterPatch Membrane Test sets the pulse first level amplitude (V1) relative to ‘V-holding’, and the pulse second level amplitude (V2) at ‘V-holding’.
Page 489: Figure 0-2. Idealized Membrane Circuit
The access resistance Ra is derived, < ground > Figure 0-2. Idealized Membrane Circuit Tau / Cm = (Ra * Rm) / (Ra + Rm) (Ra + Rm) * (Tau/Cm) = Ra * Rm Substituting in above for resistance terms: Rt = Ra + Rm Rm = Rt - Ra Rt * (Tau/Cm) = Ra * (Rt –...
Page 490: Figure 0-3. Membrane Charge
Rt = Ra + Rm Rm = Rt - Ra Cell capacitance measurements are derived from the “area under the curve” charge calculations. Figure 0-3. Membrane Charge The total charge (Qt) is composed of three parts: Main charge: The area between a response transient and its steady-state response (I1).
Page 491: Rs Correction
Qt = Q1 + Q2 The main charge (Q1) under the response transient is integrated. However, first the baseline steady-state response current (I1) is subtracted from the maxi- mum peak response (Ip), so only the current difference (Id) is integrated: Id = Ip –...
Page 492: Standard Error Of The Mean (Sem) Algorithm
Linear Exponential Fit y = y0 + A * exp( -( x – x0 ) / tau Logarithmic Exponential Fit y = k0 + k1 * exp( -( ln ( x / k2 ) / k3)^2 ) Standard Error of the Mean (SEM) Algorithm [ for Analysis Editor Error Bars ] ‘Standard Error of the Mean’...

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