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imec NEUROPIXELS 1.0 NHP LONG User Manual

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NEUROPIXELS 1.0 NHP LONG
User Manual
November 7, 2023

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  • Page 1 NEUROPIXELS 1.0 NHP LONG User Manual November 7, 2023...
  • Page 2 TERMS AND CONDITIONS OF SALE OF NEUROPIXELS 1.0 PROBES”. Imec is a registered trademark for the activities of IMEC International (a legal entity set up under Belgian law as a “stichting van openbaar nut”), imec Belgium (IMEC vzw supported by the Flemish Government), imec the Netherlands (Stichting IMEC Nederland, part of Holst Centre which is supported by the Dutch Government), imec China (IMEC Microelectronics (Shanghai) Co.
  • Page 3 List of abbreviations Action Potential. Application Programming Interface. ASIC Application Specific Integrated Circuit. BIST Built-In Self-Test. CMOS Complementary Metal-Oxide-Semiconductor. De-Ionized Water. EEPROM Electrically Erasable Programmable Read-Only Memory. Electro-Static Discharge. Flexible Printed Circuit. FPGA Field Programmable Gate Array. Ground. Headstage. Headstage Test Dongle. Identification.
  • Page 4 Definitions of technical terms ASIC: Integrated circuit that contains recording electrodes, amplifiers, multiplexers • and digitizers. Probe Shank: Implanted part of the probe ASIC. • Probe Base: Non-implanted part of the probe ASIC. • Flex: Flexible PCB (or FPC) onto which the probe ASIC and additional passive and •...

  • Page 5: Table Of Contents

    Table of Contents ABOUT THIS MANUAL ..........................6 RELATED DOCUMENTATION ......................... 6 GETTING STARTED ...........................7 UNPACKING AND HANDLING ........................ 7 HARDWARE & SYSTEM REQUIREMENTS ....................7 PXIe acquisition module control system ................... 7 OneBox control system ........................10 DRIVERS ............................... 11 PXIe acquisition module control system ..................

  • Page 6: About This Manual

    1 About This Manual This document describes the key features of the Neuropixels 1.0 probe and control system and how to install them prior to use. The Neuropixels hardware consists of: The Neuropixels probe. • The Neuropixels control system which contains: •...

  • Page 7: Getting Started

    2.2 Hardware & System Requirements PXIe acquisition module control system Figure 1 shows the Neuropixels 1.0 probe and the PXIe acquisition module control system that can be purchased from imec through www.neuropixels.org. To get started you need: one PXIe acquisition module (PXIE_1000), •...
  • Page 8 In addition, the PXIe chassis required for using the PXIe acquisition module must be purchased separately from third-party suppliers such as National Instruments (NI) Keysight or Adlink . Below we provide recommendations for PXIe chassis using a remote controller (MXI-Express interface) and a PXIe chassis with built-in Thunderbolt 3 remote controller (link).
  • Page 9 Table 1: Data acquisition configurations Config PXI-chassis Remote controller Data Acquisition Bandwidth Name Name Name Thunderbolt NI PXIe- 787026-01 Imec PXIe_1000 2 GB/s 1083 card Thunderbolt NI PXIe- 781368-01 PXIe-8301 785679-01 Imec PXIe_1000 2.3 GB/s (Figure 2) 1071 card PXIe-PCIe...

  • Page 10: Onebox Control System

    PXIe-1082 PXIe-8381 PCIe-8381 Figure 3: PXIe-8381 (remote control module) and PCIe-8381 (host interface card) allow desktop PC control of a PXI Express chassis with PCI Express Gen 2 x8 data throughput. A host PC is needed for recording the neuronal data. Make sure the following PC specifications are fulfilled: •...

  • Page 11: Drivers

    2.3 Drivers PXIe acquisition module control system To install the Neuropixels PXIe acquisition module you need to download the following PXIe Acquisition Module driver files from the SpikeGLX GitHub site. EnPcieDriverWin.inf • EnPcieDriverWin.sys • WdfCoInstaller01009.dll • enpciedriverwin.cat • Version_1.9_readme.txt • Section 4.1.3.2 of this User Manual describes how to install the driver.

  • Page 12: Developing New Software

    User Manual and User Documentation of SpikeGLX and Open Ephys. In case you lost the calibration files of your probes or in case the WeTransfer link expired, please contact neuropixels.sales@imec.be . They will provide you with the correct calibration files.

  • Page 13: Neuropixels Hardware Description

    3 Neuropixels Hardware Description 3.1 Probe The Neuropixels 1.0 NHP LONG probe (Figure 4) is a silicon CMOS digital integrated microsystem and tool for in vivo neuroscience research in large animals. The probe features 4416 low-impedance TiN recording sites densely tiled along a thin, 45 mm-long, straight shank.
  • Page 14 Avoid any damage to the wider middle section of the flex since this can render the probe non-functional. Figure 4: Left: Bare die of the Neuropixels 1.0 NHP LONG probe ASIC. Right: SEM image of the probe tip with marked electrode pitch and exposed materials. Bottom: Packaged probe ASIC with aluminum dovetail cap covering the probe base.
  • Page 15 HHMI Janelia Research Campus. The HHMI design is manufactured at imec and can be purchased via the RFQ form under the order code HOLDER_1000_C. The holder is compatible with Neuropixels 1.0 probes with Cap and with Neuropixels 1.0 NHP probes.
  • Page 16 Figure 7: Neuropixels 1.0 probe with Cap and the Figure 8: Neuropixels 1.0 probe mounted on the dove tail holder (HOLDER_1000_C) dedicated dove tail holder (HOLDER_1000_C) Figure 9: Probes with aluminum cap featuring dedicated dovetail structures. A black epoxy (EPO-TEK/H70E) encapsulates the probe perimeter and bond wires. The SMD components are also coated with a conformal, hermetic coating (ELPEGUARD/SL 1307 FLZ-T).

  • Page 17: Headstage

    NOTE : Please carefully read and follow the guidelines on soldering (Appendix B) before soldering separate wires to the REF and GND input pads. It is advisable to have prior experience in soldering before soldering to the Neuropixels probes. NOTE : Please carefully read and follow the instructions on probe handling (Appendix A) and ESD protection (Appendix C) prior to handling any Neuropixels system components.

  • Page 18: Interface Cable

    The headstage is covered with a layer of conformal coating. Some parts are not covered to keep electrical contact possible. The area of the headstage, which is not covered in conformal coating, is indicated in Figure 11 below. The ZIF connector and the Omnetics connector are not covered.

  • Page 19: Pxie Acquisition Module

    Table 7: Key cable specifications TWISTED-PAIR DATA/POWER CABLE LENGTH WEIGHT 5 g (excl. USB-C connector) DIAMETER 0.41 × 0.82 mm HEADSTAGE CONNECTOR 4-pin (Omnetics) PXIE CARD CONNECTOR USB-C WIRE STRANDS 1 twisted pair NOTE : Avoid repeated sharp bending of the cable (≤ 2 cm bending radius) as this may degrade cable quality and signal integrity.
  • Page 20 Figure 13: Top: PXIe acquisition module. Bottom: Front panel of the module. The front panel of the PXIe acquisition module (Figure 13, bottom) contains the following connectors and status LEDs: Four numbered USB-C ports allow connection of up to 4 probes. Interface cables •...

  • Page 21: Onebox

    A battery connector to supply power to the probe and HS. The use of this connector • is optional. The hardware automatically detects if an external supply is connected and, if so, switches the port supply from internal system supply to external supply. Connect a 4.0-to-5.0 V battery.
  • Page 22 Figure 14: Headstage test dongle with flex cable that plugs into the ZIF connector of a headstage. Verifying the HS functionality is one of the first steps when identifying the root cause(s) for observed failures. The HS tests are integrated in the application software (Open Ephys, SpikeGLX).

  • Page 23: Installation And Configuration

    4 Installation and Configuration 4.1 PXIe acquisition module control system This Chapter describes how to install and operate the Neuropixels Control System using a remote controller interface or a Thunderbolt configuration. Thunderbolt installation Make sure you have the following hardware components available: Third-party PXIe chassis + thunderbolt controller (see Section 2.2 for provider •...
  • Page 24 Figure 16: PXIe chassis slot symbols (source: ni.com). 3. Push the ejector handle down (Figure 17Figure 20) by pressing the grey button (step 1) on the handle and subsequently pushing the black handle (step 2) down. Figure 17: Push the ejector latch down prior to inserting the module. 4.

  • Page 25: Pxie Chassis And Remote Controller

    Figure 18: Push the ejector latch up to plug the BS module into the backplane connectors. 5. Secure the PXIe module with the mounting screws on the front panel. 6. Plug one side of the thunderbolt cable in the thunderbolt port of the PXIe 8301 module and connect the other side to a thunderbolt port on the PC.
  • Page 26 2. Identify a valid PXIe slot and remove the filler panel. The slot type on the chassis can be identified by symbols next to the slot number, as shown in Figure 19. The PXIe-8398 remote control module must be plugged into the ‘PXIe Controller Slot’. Figure 19: PXIe chassis slot symbols (source: ni.com).
  • Page 27 Figure 21: Push the ejector latch up to plug the BS module into the backplane connectors 5. Secure the PXIe module with the mounting screws on the front panel. 6. Power off and unplug your host computer. Remove the top cover or access port to the PCIe expansion slots. 8.

  • Page 28: Neuropixels Hardware

    Figure 23: NI PCIe-8398 board plugged into the PC. Neuropixels Hardware All Neuropixels system hardware is delivered preconfigured by imec. No further configuration is required. An update procedure is available for the PXIe acquisition module in case an update of the FPGA firmware code is required. The full procedure to update the FPGA firmware is described on the website of SpikeGLX.
  • Page 29 Figure 24: Global status LED of the PXIe acquisition module switching from red to green after correct installation. 4.1.3.2 Drivers After mounting the PXIe acquisition module into the chassis, install the Enclustra FPGA driver files that you have downloaded as described in Section 2.3. A detailed procedure with screenshots on how to install the driver on a Windows 10 machine is given below.
  • Page 30 Figure 25: Windows 10: Device Manager before driver installation. 2. Right click ‘PCI Memory Controller’. Click ‘Properties’. 3. Click ‘Change settings’ Figure 26: Windows 10: Uninstalled device properties. 4. Click ‘Update Driver...’ NEUROPIXELS 1.0 NHP USER MANUAL V1.0.1...
  • Page 31 Figure 27: Windows 10: Editable device properties. 5. Click ‘browse My computer for driver software’ Figure 28: Windows 10: Install driver. 6. Browse to the location with the driver files. Click ‘Next’. NEUROPIXELS 1.0 NHP USER MANUAL V1.0.1...
  • Page 32 Figure 29: Windows 10: Select driver file. If all goes well, you get a screen saying that Windows has successfully updated your driver. Click ‘Close’. Figure 30: Windows 10: Successful driver update confirmation. 8. Click ‘Close’. NEUROPIXELS 1.0 NHP USER MANUAL V1.0.1...
  • Page 33 Figure 31: Windows 10: Device properties after installation. 9. Reboot the PC and log in with a normal user account. Check the installation of the driver in the Device Manager. After successful installation, an Enclustra PCI Express Adapter shows up in the Device Manager under Enclustra Devices. Figure 32: Windows 10: Device manager after installation.
  • Page 34 4. After your PC restarts to the Choose an option screen (step 1 below), select Troubleshoot (step 2) > Advanced options (step 3) > Startup Settings (step 4) > Restart. 5. After your PC restarts, select ‘7’ or ‘F7’, your PC will automatically reboot with the new startup setting.
  • Page 35 STEP C Step D 3. After your PC restarts, press ‘7’ or ‘F7’ (Step E), your PC will automatically reboot with the new startup setting. Step E PRESS ‘7’ or ‘F7’ An unsuccessful installation of the driver can also be fixed by uninstalling and reinstalling the driver.

  • Page 36: Onebox

    4.1.3.3 Remote FPGA update The PXIe acquisition module is always shipped with the latest firmware release programmed on the board. However, firmware updates which extend the functionality of the PXIe acquisition module will be released. Updating the firmware on the board can be done with the application software packages SpikeGLX or Open Ephys.

  • Page 37: Using The System

    5 Using the System 5.1 Connecting the System Components Probe to HS The probe flex connects to the HS via the ZIF connector (Figure 33, right). To plug the flex into the HS, gently lift the black latch of the HS ZIF connector (Figure 33, left). If the HS ZIF connector faces up, the gold contacts on the flex cable (Figure 6, right) must face down.

  • Page 38: Electrode Selectivity

    Loading of probe-specific configuration files (these files are provided by imec with • every probe shipment through a file transfer service. In case you lost the calibration files please contact neuropixels.sales@imec.be.) Reading of serial numbers, part numbers, hardware versions, and software versions.
  • Page 39 El 4414 El 4415 El 4224 El 4225 El 4222 El 4223 El 3840 El 3841 El 3838 El 3839 El 3456 El 3457 El 3454 El 3455 El 3072 El 3073 El 3070 El 3071 El 2688 El 2689 El 2686 El 2687 El 2304...

  • Page 40: Reference Selection

    Reference Selection Three reference inputs are available for each channel: External reference: multiple input pads are located on the probe flex. Separate wires • can be soldered to these pads. Tip electrode: a large TiN electrode located at the tip of the shank. •...

  • Page 41: Support And Troubleshooting

    Neuropixels probes. This will be the fastest and most efficient mechanism for you to resolve issues with your Neuropixels probes. Please do not contact imec directly at any of the generic imec email contact information addresses.

  • Page 42: Headstage Test Dongle

    Select the correct Slot, Port and Dock and press “Go”. This will run all defined tests by • default. Be aware the noise test may fail since you are testing the probe in suboptimal conditions. Headstage Test Dongle The HST is a small test box (Figure 14) that plugs into the HS ZIF connector of a HS. Its purpose is to help verify the functionality of a headstage (HS).
  • Page 43 Figure 36: Setup for gain measurements in PBS. Noise measurements should always be performed in a grounded Faraday cage. One can use either an internal REF electrode or the external REF shorted to GND. The reference selection is done via the GUI. The PBS solution must be grounded (Figure 37Figure 36). During noise measurements, all internal REF electrodes must be immersed in PBS to avoid unwanted noise pick-up and cross-coupling.

  • Page 44: Frequently Asked Questions

    Q5: I want to place an order for probes and system parts. How do I proceed? A5: Please download the RFQ form on the website. Fill in all the details and quantities and send the document to neuropixels.sales@imec.be. They will provide an official quotation which needs to be signed.
  • Page 45 Q8: The imec data acquisition card PXIe_1000 does not show up in the NI MAX tool? A8: It’s correct that the imec data acquisition card does not show up in the NI MAX tool. This does not mean that the card is dysfunctional.

  • Page 46: Probe Handling, Cleaning, Storage

    Probe Handling, Cleaning, Storage Please follow these guidelines to remove the probes from the shipping box: Wear gloves to minimize dust and dirt contamination. Work in a clean environment. • Carefully open the box with the lid pointing away from you. This way the shanks are •...
  • Page 47 Take a pair of ESD-safe tweezers and carefully clamp the base of the probe as shown • in Figure 40. Carefully pick up the probe while keeping the foam pushed open. • At all times, keep your eyes on the shank and make sure that it does not touch the •...
  • Page 48 Figure 40: Removing the probe from the shipping box Please follow these guidelines to ensure mechanical integrity of the fragile shank, electrodes and flex: Do not touch the shank with your fingers or other objects. • Do not subject the probe to vibrations (potential damage of TiN electrodes and •...
  • Page 49 Deionized water (DIW) at room temperature Iso-propyl alcohol (IPA) Phosphate buffered saline (PBS) @ pH 7.4 (https://www.sigmaaldrich.com/content/dam/sigma- aldrich/docs/Sigma/Datasheet/pbs1dat.pdf) 25 mM MOPS (3-(N-morpholino)propanesulfonic acid) (http://www.sigmaaldrich.com/catalog/product/sigma/m1254?lang=en&re gion=BE), 150 mM NaCl, DI water, pH adjusted w/ NaOH and HCl 100 mM MES (2-ethanesulfonic acid) (https://www.sigmaaldrich.com/BE/en/product/fluka/69889), 150 mM NaCl, DI water, pH adjusted w/ NaOH and HCl Tergazyme...

  • Page 50: Soldering

    Soldering If the experiment requires a connection to the ground and/or external reference signal, the user can make use of the two GND and REF arms which are part of the probe flex. In case these arms are not usable as such, the user can extend or replace these by soldering wires to the provided solder pads on the flex.
  • Page 51 Figure 42: Placing the solder tip in the corner between wire and pad. Feed a small amount of solder to the corner between the solder tip and wire. The • solder melts on the pad and the GND/REF wire. Solder wire can be purchased in different diameters.
  • Page 52 Figure 44: Solder applied to solder pad and GND/REF wire separately. Place the GND/REF wire on top of the solder pad. • Press the solder tip on top of the GND/REF wire and feed some amount of solder • wire. This forms a strong solder joint. (Figure 45) Figure 45: Soldered wire to solder pad without hole.

  • Page 53: Esd Safety

    ESD Safety To avoid ESD damage when handling the electronic hardware (probe, HS, PXIe, OneBox), the operator must be grounded via ESD protective equipment, such as a wrist wrap. General ESD guidelines can be found at: http://www.esda.org/about-esd/esd-fundamentals/part-3- basic-esd-control-procedures-and-materials/. When the probe is implanted in an animal, special precautions are required; To protect the probe from ESD damage, potential static charge build-up on the animal must be discharged via a low-current path.

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