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NEUROPIXELS 1.0 HD
User Manual
June 19, 2024

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  • Page 1 NEUROPIXELS 1.0 HD User Manual June 19, 2024...
  • 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 Printed Circuit Board. Personal Computer. PCIe Peripheral Component Interconnect Express. PXIe PCI eXtensions for Instrumentation express. (External) Reference. Room Temperature. Scanning Electron Microscope. Sub-Miniature version A. Surface-Mount Devices. USB-C Universal Serial Bus Type-C. Zero Insertion Force. NEUROPIXELS 1.0 HD USER MANUAL V1.0...
  • Page 4 • Driver: The software files that need to be installed on the host PC to enable communication with the Neuropixels control system and to develop custom application software. NEUROPIXELS 1.0 HD USER MANUAL V1.0...

  • Page 5: Table Of Contents

    Built-In Self-Tests ..........................42 5.3.3 Headstage Test Dongle ........................43 5.3.4 Gain and Noise Measurements ....................... 43 5.3.5 Frequently asked questions......................45 PROBE HANDLING, CLEANING, STORAGE ................47 SOLDERING ........................51 ESD SAFETY ........................54 NEUROPIXELS 1.0 HD USER MANUAL V1.0...

  • Page 6: About This Manual

    1 About This Manual This document describes the key features of the Neuropixels 1.0 HD 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 2.2.1 PXIe acquisition module control system Figure 1 shows the Neuropixels 1.0 HD probe and the PXIe acquisition module control system that can be purchased from imec through www.neuropixels.org. To get started you need: •...
  • Page 8 MXI-Express interface: NI PCIe-8389 and PXIe-8389 (Gen 3 x16, 1 Port; incl. one MXI- • Express x16 copper cable, 3m). PN 784177-01 Other chassis-remote controller combinations are technically possible. A list of combinations is given in Table 1 below: https://ohm.ni.com/advisors/pxi/pages/common/intro.xhtml https://www.keysight.com/us/en/home.html https://www.adlinktech.com/en/index NEUROPIXELS 1.0 HD USER MANUAL V1.0...
  • Page 9 2.3 GB/s (Figure 3) 1082 8381 card PXIe-PCIe NI PXIe- 781368-01 PXIe-PCIe End of life Imec PXIe_1000 2.3 GB/s 1071 8381 card OneBox ONE_1000 USB 3.0 Figure 2: PXIe chassis PXIe-1071 & Thunderbolt PXIe-8301 NEUROPIXELS 1.0 HD USER MANUAL V1.0...

  • Page 10: Onebox Control System

    NOTE: If you decide to use the existing application software packages SpikeGLX or Open Ephys described in Section 2.4.1, please consult the respective software User Manual and/or online Documentation to ensure you also comply with these system requirements. 2.2.2 OneBox control system Coming soon NEUROPIXELS 1.0 HD USER MANUAL V1.0...

  • Page 11: Drivers

    OneBox control system Coming soon 2.4 Application Software 2.4.1 Existing Software You can acquire data from Neuropixels 1.0 HD probes with either of two existing software packages: SpikeGLX Open Ephys . The former is being developed by Bill Karsh at Janelia Research Campus.

  • 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. NEUROPIXELS 1.0 HD USER MANUAL V1.0...

  • Page 13: Neuropixels Hardware Description

    3 Neuropixels Hardware Description 3.1 Probe The Neuropixels 1.0 HD probe is a silicon CMOS digital integrated microsystem and tool for in vivo neuroscience research in small animals. The probe features 6144 low-impedance TiN recording sites densely tiled along a thin, 10 mm-long, straight shank. The 384 parallel, configurable, low-noise recording channels integrated in the base enable simultaneous, dual-band recording of hundreds of neurons.
  • Page 14 ~15 mW (in recording mode; typical) SHANK HEATING <1°C (in the brain) The probe ASIC is packaged (glued and wirebonded) on a flexible polyimide printed circuit board populated with several SMD components (Figure 4). The components include Process corner NEUROPIXELS 1.0 HD USER MANUAL V1.0...
  • Page 15 NOTE: Please be careful when cutting the narrow side arms of the flex. Use a pair of fine, pointed scissors. Avoid any damage to the wider middle section of the flex since this can render the probe non-functional. NEUROPIXELS 1.0 HD USER MANUAL V1.0...
  • Page 16 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 (HD) probes, Neuropixels 1.0 probes with Cap and with Neuropixels 1.0 NHP probes.
  • Page 17 Figure 7: Neuropixels 1.0 HD probe with Cap and Figure 8: Neuropixels 1.0 HD probe mounted on the dove tail holder (HOLDER_1000_C) the 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 18: Headstage

    API call. A HS EEPROM contains information on serial number (as printed on the label), part number, PCB version and revision number. Table 6 summarizes the key headstage specifications. Table 6: Key headstage specifications HEADSTAGE SIZE 15  16 mm NEUROPIXELS 1.0 HD USER MANUAL V1.0...

  • Page 19: Interface Cable

    HS and transfers control and neural data to/from the HS. The cable assembly weighs 5 g (excl. USB-C connector) and consists of two 5-m long wire strands each having a diameter of 0.41 mm. NEUROPIXELS 1.0 HD USER MANUAL V1.0...

  • Page 20: Pxie Acquisition Module

    It is compatible with a standard PXIe chassis, which must be purchased from other well-known third-party vendors such as NI, Keysight or Adlink. Chassis recommendations are provided in Section 2.2 . Custom cable assembly. Xilinx ZYNQ and Xilinx Artix-7 NEUROPIXELS 1.0 HD USER MANUAL V1.0...
  • Page 21 A trigger line switch matrix and configurable sync clock are implemented. Various trigger signals can be programmed: SMA connector, 7 trigger lines on the PXIe bus, user defined data or software trigger. Common trigger for multiple modules and/or external instruments. NEUROPIXELS 1.0 HD USER MANUAL V1.0...

  • Page 22: Onebox

    Its purpose is to help verify the functionality of a HS. This is useful when e.g. neural data seems corrupt or cannot be recorded or when a probe cannot be programmed correctly anymore. NEUROPIXELS 1.0 HD USER MANUAL V1.0...
  • Page 23 If such a short would occur without being detected by the HST, the neural data recorded by the probe will be corrupted on multiple channels. Figure 15: Locations on the HS in which an electrical short-circuit cannot be detected. NEUROPIXELS 1.0 HD USER MANUAL V1.0...

  • Page 24: Installation And Configuration

    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-8301 thunderbolt module must be plugged into the ‘PXIe Controller Slot’. NEUROPIXELS 1.0 HD USER MANUAL V1.0...
  • Page 25 4. Slide the module into the PXIe slot. Observe the correct orientation of the module. When the ejector handle touches the metal rail of the chassis, lift the ejector handle to push the module into the slot for the last few millimeters. NEUROPIXELS 1.0 HD USER MANUAL V1.0...

  • Page 26: Pxie Chassis And Remote Controller

    Follow the steps below to install the PXIe-8398 remote controller into the NI PXIe-1071 chassis and the NI PCIe-8398 board into the PC: Power-off the PXIe chassis but leave the power cable plugged in to ground the chassis. NEUROPIXELS 1.0 HD USER MANUAL V1.0...
  • Page 27 4. Slide the module into the PXIe slot. Observe the correct orientation of the module. When the ejector handle touches the metal rail of the chassis, lift the ejector handle to push the module into the slot for the last few millimeters. NEUROPIXELS 1.0 HD USER MANUAL V1.0...
  • Page 28 13. Connect the MXI-Express x16 cable to both MXI-Express x16 cards. The cables have no polarity, so you can connect either end to either card. Continue with step 14 in section 4.1.3.1 further below. Figure 22: PCIe x16 slot on the PC motherboard. NEUROPIXELS 1.0 HD USER MANUAL V1.0...

  • Page 29: Neuropixels Hardware

    4.1.3 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 30 Start the Windows Device Manager with an administrator account. The example in the screenshot below shows the device manager for a chassis with one base station plugged in, prior to installation. The PXIe acquisition modules show up as PCI Memory Controller under Other devices. NEUROPIXELS 1.0 HD USER MANUAL V1.0...
  • Page 31 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 HD USER MANUAL V1.0...
  • Page 32 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 HD USER MANUAL V1.0...
  • Page 33 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 HD USER MANUAL V1.0...
  • Page 34 To start Windows 10 in safe mode or get to other startup settings: Select the Start button, then choose Settings 2. Select Update & security > Recovery. 3. Under Advanced startup select Restart now. NEUROPIXELS 1.0 HD USER MANUAL V1.0...
  • Page 35 (in the lower-right corner of the screen). 2. After your PC restarts to the Choose an option screen, select Troubleshoot (step A) > Advanced options (Step B) > Startup Settings (Step C) > Restart (Step D). STEP A STEP B NEUROPIXELS 1.0 HD USER MANUAL V1.0...
  • Page 36 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. NEUROPIXELS 1.0 HD USER MANUAL V1.0...

  • Page 37: Onebox

    PXIe chassis. You can use a pen to press the switch. Keep the switch pressed for a few seconds, until the STATUS led lights up as green. The update procedure can now be repeated from the application software. 4.2 OneBox Coming soon NEUROPIXELS 1.0 HD USER MANUAL V1.0...

  • Page 38: Using The System

    The Neuropixels API provides various functionalities to control, configure and test the probe and control system, including (but not limited to): Selection of recording electrodes, reference inputs, channel gains, and bandwidth. • • Selection of trigger mode. NEUROPIXELS 1.0 HD USER MANUAL V1.0...

  • Page 39: 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 40 Swapped which repeat alternately across the shank. With this layout in mind, the selection possibilities are shown in Figure 36Error! Reference source not found. and allow for both a compact 848 selection and an elongated 2192 selection. NEUROPIXELS 1.0 HD USER MANUAL V1.0...

  • Page 41: Reference Selection

    Internal reference electrode: a large TiN electrode located at the tip of the shank. • External reference electrode: multiple input pads are located on the probe flex. • Separate wires can be soldered to these pads (see also Figure 5). Figure 37: Visualization of the reference options. NEUROPIXELS 1.0 HD USER MANUAL V1.0...

  • Page 42: 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 43: Headstage Test Dongle

    The resulting mean gain should not deviate >10% from the nominal value and at least 90% of the electrodes should have a gain within 5% of the mean gain. The results can provide qualitative and quantitative information about electrodes and/or channel performance. NEUROPIXELS 1.0 HD USER MANUAL V1.0...
  • Page 44 The nominal gain for both AP and LFP channels should be set to 1000. To obtain the actual input-referred noise, one must divide the measured noise by the actual gain measured above. Figure 39: Setup for noise measurements in PBS. NEUROPIXELS 1.0 HD USER MANUAL V1.0...

  • Page 45: Frequently Asked Questions

    Q7: The imec data acquisition card PXIe_1000 does not show up in the NI MAX tool? 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 A good description is given on this website: https://github.com/billkarsh/SpikeGLX/blob/master/Markdown/SystemRequirements_PXI.m NEUROPIXELS 1.0 HD USER MANUAL V1.0...

  • Page 47: Probe Handling, Cleaning, Storage

    Up to six probes are shipped in each box. • We advise to remove probes only from the leftmost non-empty slot not to • accidentally touch the other probes. Figure 40: Removing the probe from the shipping box. NEUROPIXELS 1.0 HD USER MANUAL V1.0...
  • Page 48 Figure 41: Removing the probe from the shipping box (foam with vertical slits) Figure 42: Removing the probe from the shipping box (foam with vertical slits) Please follow these guidelines to ensure mechanical integrity of the fragile shank, electrodes and flex: NEUROPIXELS 1.0 HD USER MANUAL V1.0...
  • Page 49 Rinsing or prolonged soaking of Neuropixels probes in DIW (pH ≈ 5.7) does not deteriorate the TiN impedance; if anything, the impedance slightly decreases after prolonged soaking (likely due to improved wetting). DIW degassing is not needed. NEUROPIXELS 1.0 HD USER MANUAL V1.0...
  • Page 50 DIW should be applied at the end. Rinse the probes with IPA and let dry in air. Store the probes in the black ESD safe shipping boxes at room temperature. NEUROPIXELS 1.0 HD USER MANUAL V1.0...

  • Page 51: Soldering

    Wet the solder tip slightly with solder wire. This improves heat transfer from the iron • to the solder pad. Insert the wire through the hole in the solder pad. Place the solder iron at the corner • between the pad and the GND/REF wire. (Figure 44) NEUROPIXELS 1.0 HD USER MANUAL V1.0...
  • Page 52 Figure 45: Wire soldered to the solder pad. An alternative method does not make use of the hole in the solder pad: Apply some solder to the solder pad and GND/REF wire separately. (Figure 46) • NEUROPIXELS 1.0 HD USER MANUAL V1.0...
  • Page 53 Please consult this website on best practices on soldering: Noise: Learn How To Solder - SpikeGLX (billkarsh.github.io). NEUROPIXELS 1.0 HD USER MANUAL V1.0...

  • Page 54: Esd Safety

    HS. This is normally already achieved if the PXIe chassis is plugged into the mains supply. NOTE: A connection from the probe to the PXIe acquisition module ground does not provide an ESD-safe discharge path, because it does not contain a current-limiting resistor. NEUROPIXELS 1.0 HD USER MANUAL V1.0...

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