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imec NEUROPIXELS 1.0 User Manual

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NEUROPIXELS 1.0
User Manual
February 13, 2020

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Summary of Contents for imec NEUROPIXELS 1.0

  • Page 1 NEUROPIXELS 1.0 User Manual February 13, 2020...
  • Page 2 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 Taiwan (IMEC Taiwan Co.) and imec China...
  • 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 USER MANUAL V1.0.5...
  • Page 4 PXIe Chassis: Houses PXIe modules and connects them with a high-performance backplane that • offers timing and synchronization capabilities. 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 USER MANUAL V1.0.5...

  • Page 5: Table Of Contents

    SUPPORT AND TROUBLESHOOTING ....................36 Visual Inspection ..........................36 Built-In Self-Tests ..........................36 Headstage Test Dongle ........................37 Gain and Noise Measurements ....................... 37 PROBE HANDLING, CLEANING, STORAGE ................39 SOLDERING ........................... 42 ESD SAFETY ........................... 45 NEUROPIXELS 1.0 USER MANUAL V1.0.5...

  • Page 6: About This Manual

    A headstage test dongle. • Even if you have read articles on the Neuropixels 1.0 probes and feel that you are familiar with using User the Neuropixels probes we request and encourage you to carefully read the latest version of this...

  • Page 7: Getting Started

    Carefully read the guidelines on probe handling (Appendix A), soldering (Appendix B) and ESD safety (Appendix C). 2.2 Hardware & System Requirements Figure 1 shows the Neuropixels 1.0 probe and control system that can be purchased from imec through www.neuropixels.org or www.neuropixels.info. To get started you need: one PXIe acquisition module, •...
  • Page 8 October 2018) NI part number: 782522-01 (http://ohm.ni.com/advisors/pxi/pages/common/intro.xhtml, October 2018) NI part number: 780321-01 (http://ohm.ni.com/advisors/pxi/pages/common/intro.xhtml, October 2018) NI part number: 763000-01 (US), 763067-01 (EU), 763064-01 (UK) (http://ohm.ni.com/advisors/pxi/pages/common/intro.xhtml, October 2018) NI part number: 782522-01 (http://ohm.ni.com/advisors/pxi/pages/common/intro.xhtml, October 2018) NEUROPIXELS 1.0 USER MANUAL V1.0.5...

  • Page 9: Drivers

    User Manual describes how to install the driver. 2.4 Application Software Existing Software You can acquire data from Neuropixels 1.0 probes with either of two existing software packages: SpikeGLX Open Ephys . The former is being developed by Bill Karsh at Janelia Research Campus.

  • Page 10: Probe Configuration Files

    These files are essential to correct for CMOS processing-induced deviations of probe performance. User Details on how to load these files into the application software are described in the respective Manual User Documentation of SpikeGLX and Open Ephys. NEUROPIXELS 1.0 USER MANUAL V1.0.5...

  • Page 11: Neuropixels Hardware Description

    3 Neuropixels Hardware Description 3.1 Probe The Neuropixels 1.0 probe (Figure 3) is a fully-integrated silicon CMOS ASIC with on-chip circuitry for signal conditioning and digitization. The probe features 960 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 12 Figure 3: Top left: Bare die of the Neuropixels probe ASIC. Bottom left: Two SEM images of the probe tip with marked electrode pitch and exposed materials. Right: Packaged probe ASIC with silicon spacer covering the probe base. The SMD components are assembled on the flex base. NEUROPIXELS 1.0 USER MANUAL V1.0.5...
  • Page 13 HHMI Janelia Research Campus. Probes with metal cap are available as of June 2019. NEUROPIXELS 1.0 USER MANUAL V1.0.5...

  • Page 14: Headstage

    The HS (Figure 7) is 16  15 mm and weighs 0.9 g. It contains several LDO regulators for power supply, a serializer chip for communication to/from the PXIe acquisition module, and an EEPROM for NEUROPIXELS 1.0 USER MANUAL V1.0.5...

  • Page 15: 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. Figure 8: Twisted-pair interface cable with Omnetics-to-USB-C termination NEUROPIXELS 1.0 USER MANUAL V1.0.5...

  • Page 16: Pxie Acquisition Module

    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 USER MANUAL V1.0.5...
  • Page 17 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. A SYNC/TRIGGER I/O SMA connector: • NEUROPIXELS 1.0 USER MANUAL V1.0.5...

  • Page 18: Headstage Test Dongle

    NOTE: The API provides several built-in self-tests described in the Troubleshooting Section 5.3. These can be implemented in the application software and help diagnose and debug potential hardware failures along the entire signal chain from ASIC to PC. NEUROPIXELS 1.0 USER MANUAL V1.0.5...
  • Page 19 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 11: Locations on the HS in which an electrical short-circuit cannot be detected. NEUROPIXELS 1.0 USER MANUAL V1.0.5...

  • Page 20: Installation And Configuration

    Figure 12: PXIe chassis slot symbols (source: ni.com). 3. Push the ejector handle down (Figure 13) by pressing the grey button (step 1) on the handle and subsequently pushing the black handle (step 2) down. NEUROPIXELS 1.0 USER MANUAL V1.0.5...
  • Page 21 12. Replace the computer cover. 13. Connect the MXI-Express x8 cable to both MXI-Express x8 cards. The cables have no polarity, so you can connect either end to either card. Continue with step 14 further below. NEUROPIXELS 1.0 USER MANUAL V1.0.5...

  • Page 22: Neuropixels Hardware

    Figure 16: NI PCIe-8381 board plugged into the PC. 4.2 Neuropixels Hardware All Neuropixels system hardware is delivered preconfigured by IMEC. No further configuration is required. A remote update procedure is available for the PXIe acquisition module in case an update of the FPGA firmware code is required.

  • Page 23: Drivers

    1. Start the Windows Device Manager with an administrator account. The example in the screenshot below shows the device manager for a chassis with one basestation plugged in, prior to installation. The PXIe acquisition modules show up as PCI Memory Controller under Other devices. NEUROPIXELS 1.0 USER MANUAL V1.0.5...
  • Page 24 2. Right click on ‘PCI Memory Controller’. Select Úpdate driver software’. 3. Click ‘Browse my computer for driver software’. Figure 19: Windows 7: Install driver. 4. Browse to the location with the driver files. Click ‘Next’. NEUROPIXELS 1.0 USER MANUAL V1.0.5...
  • Page 25 Figure 20: Windows 7: Select driver file. 5. A warning screen pops up. Click ‘Install’. Figure 21: Windows 7: Confirm driver installation. 6. If all goes well, you should get a confirmation that the driver was successfully installed. NEUROPIXELS 1.0 USER MANUAL V1.0.5...
  • Page 26 A detailed procedure with screenshots on how to install the driver on a Windows 10 machine is given below. 1. Start the Windows Device Manager with an administrator account. The example in the screenshot below shows the device manager for a chassis with one basestation plugged in, NEUROPIXELS 1.0 USER MANUAL V1.0.5...
  • Page 27 The PXIe acquisition modules show up as PCI Memory Controller under Other devices. Figure 24: Windows 10: Device Manager before driver installation. 2. Right click ‘PCI Memory Controller’. Click ‘Properties’. 3. Click ‘Change settings’ Figure 25: Windows 10: Uninstalled device properties. 4. Click ‘Update Driver...’ NEUROPIXELS 1.0 USER MANUAL V1.0.5...
  • Page 28 Figure 26: Windows 10: Editable device properties. 5. Click ‘browse My computer for driver software’ Figure 27: Windows 10: Install driver. 6. Browse to the location with the driver files. Click ‘Next’. NEUROPIXELS 1.0 USER MANUAL V1.0.5...
  • Page 29 Figure 28: Windows 10: Select driver file. 7. If all goes well, you get a screen saying that Windows has successfully updated your driver. Click ‘Close’. Figure 29: Windows 10: Successful driver update confirmation. 8. Click ‘Close’. NEUROPIXELS 1.0 USER MANUAL V1.0.5...
  • Page 30 This occurs if Windows cannot verify the digital signature of the driver . A temporary fix is to disable the driver signature enforcement in the Windows Startup Settings. Work in progress to enable this feature. NEUROPIXELS 1.0 USER MANUAL V1.0.5...
  • Page 31 1. On the sign-in screen, hold the Shift key down while you select Power > Restart (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). NEUROPIXELS 1.0 USER MANUAL V1.0.5...
  • Page 32 STEP A STEP B STEP C NEUROPIXELS 1.0 USER MANUAL V1.0.5...

  • Page 33: Remote Fpga Update

    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. NEUROPIXELS 1.0 USER MANUAL V1.0.5...

  • Page 34: Using The System

    Selection of recording electrodes, reference inputs, channel gains, and bandwidth. • Selection of trigger mode. • Loading of probe-specific configuration files (these files are provided by imec with every probe • shipment through a file transfer service). Reading of serial numbers, part numbers, hardware versions, and software versions.

  • Page 35: Electrode Selectivity

    The reference selection is channel-independent, and each channel can only connect to one of the three reference inputs simultaneously. Moreover, the internal reference can only connect to one of the available three internal electrodes, which are spaced 3.84 mm apart. NEUROPIXELS 1.0 USER MANUAL V1.0.5...

  • Page 36: Support And Troubleshooting

    IMEC Neuropixels representative contacts the person who ordered the probes, and please correspond ONLY with the designated person from IMEC who reaches out to you. 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 37: Headstage Test Dongle

    The PBS solution must be grounded (Figure 36). During noise measurements, all internal REF electrodes must be immersed in PBS to avoid unwanted noise pick-up and cross-coupling. When using the external REF, the external REF electrode must be grounded via the REF and GND contact pads on the flex. NEUROPIXELS 1.0 USER MANUAL V1.0.5...
  • Page 38 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 37: Setup for noise measurements in PBS. NEUROPIXELS 1.0 USER MANUAL V1.0.5...

  • Page 39: Probe Handling, Cleaning, Storage

    (Figure 40). At all times, keep your eyes on the shank and make sure that it does not touch the foam. • Figure 38: Removing the probe from the shipping box. NEUROPIXELS 1.0 USER MANUAL V1.0.5...
  • Page 40 Color changes/darkening of the TiN can indicate corrosion or other damage. Please report such observations. Do not pinch the flex of the probe and maintain a minimum bending radius of 3 mm. • NEUROPIXELS 1.0 USER MANUAL V1.0.5...
  • Page 41 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 USER MANUAL V1.0.5...

  • Page 42: 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 42) NEUROPIXELS 1.0 USER MANUAL V1.0.5...
  • Page 43 Figure 43: 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 44) • NEUROPIXELS 1.0 USER MANUAL V1.0.5...
  • Page 44 IMPORTANT: Generally, poor connections are a common source of noise. The reference and ground connections on the probe and flex are critical as they are very close to the probe signal amplifiers. NEUROPIXELS 1.0 USER MANUAL V1.0.5...

  • Page 45: Esd Safety

    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 USER MANUAL V1.0.5...

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