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NEUROPIXELS 1.0

User Manual

February 13, 2020

Summary of Contents for NEUROPIXELS 1.0

Page 1: ...NEUROPIXELS 1 0 User Manual February 13 2020...

Page 2: ...n Institute for Brain Science and University College London Legal Disclaimer The contents of this document are provided by imec as is Imec makes no representations nor warranties with respect to the a...

Page 3: ...HS Headstage HST Headstage Test Dongle ID Identification I O Input and or Output IPA Isopropyl Alcohol LDO Low DropOut LED Light Emitting Diode LFP Local Field Potential MSVC Microsoft Visual C MXI Mu...

Page 4: ...he probe Figure 7 Headstage Test Dongle a small test box Figure 10 that plugs into the ZIF connector of a headstage Its purpose is to help verify the functionality of a Headstage Interface Cable Thin...

Page 5: ...ACQUISITION MODULE 16 3 5 HEADSTAGE TEST DONGLE 18 4 INSTALLATION AND CONFIGURATION 20 4 1 PXIE CHASSIS AND REMOTE CONTROLLER 20 4 2 NEUROPIXELS HARDWARE 22 PXIe Acquisition Module 22 Drivers 23 Remot...

Page 6: ...opixels probes then it is absolutely essential and imperative that you carefully read the complete User Manual Please check www neuropixels org or www neuropixels info for the latest version of this m...

Page 7: ...ering 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 w...

Page 8: ...Gen 2 x8 or wider to install the PXIe remote controller Please refer to the OpenEphys or SpikeGLX website for exhaustive PC requirements Chapter 4 in this User Manual contains further instructions on...

Page 9: ...tracellular electrophysiology data acquisition and is being developed by Josh Siegle and Jakob Voigts Both packages use the same underlying Neuropixels API to communicate with the probes so their func...

Page 10: ...to the person listed on the sales order The provided configuration files must be loaded into software prior to using the probes These files are essential to correct for CMOS processing induced deviat...

Page 11: ...SIZE 12 12 m IMPEDANCE 150 k at 1 kHz in PBS SELECTIVITY Local switch under each electrode Table 2 Shank specifications SHANK PROPERTIES AND MATERIALS NUMBER 1 WIDTH 70 m LENGTH 10 mm THICKNESS 24 m B...

Page 12: ...hen not used 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...

Page 13: ...probe ID attached to ZIF area front side Right ZIF area back side with metal contact pads The probe base is covered either with a 300 m thick silicon spacer 8 5 3 9 mm or aluminum metal cap10 7 3 4 8...

Page 14: ...H OF FLEX 39 5 mm THICKNESS AT PROBE BASE 1 2 mm w Si spacer 1 8 mm w metal cap THICKNESS OF FLEX 80 m EXTERNAL REFERENCE INPUT REF multiple pads along flex GROUND INPUT GND multiple pads along flex B...

Page 15: ...number PCB version and revision number Table 5 summarizes the key headstage specifications Table 5 Key headstage specifications HEADSTAGE SIZE 15 16 mm WEIGHT 0 9 g ZIF CONNECTOR 45 pin CABLE CONNECT...

Page 16: ...gure 9 is a custom made board with a deserializer chip and two FPGAs12 for probe configuration data acquisition and transmission to PC via a PCIe interface It is compatible with standard PXIe chassis...

Page 17: ...correctly configured o Blue An internal data emulator on the Artix 7 FPGA is active The probe data is not used A general status LED indicates the status of the PXIe module o Off The Artix 7 FPGA is no...

Page 18: ...for an ethernet connection neither FPGA code nor API currently support this functionality NOTE Please carefully read and follow the instructions on ESD protection Appendix C prior to handling any sys...

Page 19: ...etected with the HST except for 2 specific locations on the HS which are indicated in yellow on the figure below If such a short would occur without being detected by the HST the neural data recorded...

Page 20: ...l provide you with some basic guidelines but do emphasize the need to follow the instructions and safety information described in the user manuals of the chosen PXIe chassis and remote controller prov...

Page 21: ...with the mounting screws on the front panel 6 Power off and unplug your host computer 7 Remove the top cover or access port to the PCIe expansion slots 8 Select any available PCIe x8 expansion slot Fi...

Page 22: ...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...

Page 23: ...e 17 The LINK status LED of the remote controller will also turn green Figure 17 Global status LED of the PXIe acquisition module switching from red to green after correct installation Drivers After m...

Page 24: ...s 7 Device Manager before driver installation 2 Right click on PCI Memory Controller Select pdate driver software 3 Click Browse my computer for driver software Figure 19 Windows 7 Install driver 4 Br...

Page 25: ...1 0 5 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 drive...

Page 26: ...tra PCI Express Adapter shows up in the Device Manager under Enclustra Devices Figure 23 Windows 7 Device manager after installation 4 2 2 2 Install drivers on Windows 10 A detailed procedure with scr...

Page 27: ...ion 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 sett...

Page 28: ...0 USER MANUAL V1 0 5 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 fil...

Page 29: ...V1 0 5 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...

Page 30: ...vice Manager under Enclustra Devices Figure 31 Windows 10 Device manager after installation On some Windows PCs the installation of the PXIe Acquisition Module driver may fail and an exclamation mark...

Page 31: ...t Update security Recovery 3 Under Advanced startup select Restart now 4 After your PC restarts to the Choose an option screen step 1 below select Troubleshoot step 2 Advanced options step 3 Startup S...

Page 32: ...NEUROPIXELS 1 0 USER MANUAL V1 0 5 32 STEP A STEP B STEP C...

Page 33: ...ges SpikeGLX or Open Ephys However in case this update procedure would fail for example due to a power failure of the system during the update process a recovery procedure needs to be followed If the...

Page 34: ...can thus be plugged into the PXIe acquisition module in either orientation The HS side of the cable is terminated with a 4 pin Omnetics connector This connector is not symmetric and must be plugged i...

Page 35: ...channel 199 can connect to electrode 200 and 584 Table 7 Figure 34 Electrode bank distribution along the shank Table 7 Electrode channel mapping Bank number 0 Bank number 1 Bank number 2 Channel Elect...

Page 36: ...Specialist in your local geography In the unfortunate event that your probe is defective and or non functional your Neuropixels Superuser Specialist will confirm this to IMEC directly IMEC will then c...

Page 37: ...measurement in PBS solution These measurements should be performed after loading the probe configuration files into software Gain measurements must be performed using the external REF shorted to GND T...

Page 38: ...0 5 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 Setu...

Page 39: ...y lifting the foam in this orientation even the corners will never touch the shanks accidentally Up to six probes are shipped in each box We advise to remove probes only from the leftmost non empty sl...

Page 40: ...ations potential damage of TiN electrodes and shank Such vibrations could arise e g when blow drying the probe with compressed air or N2 or when subjecting the probe to ultrasound Always work in a cle...

Page 41: ...inse the probes including the electrical components under a gentle DIW stream or in a beaker for 1 2 minutes followed by IPA rinsing for 1 2 minutes Do not use a high pressure water or IPA stream Afte...

Page 42: ...cation Apply some solder to the solder tip before switching off This prevents corrosion to the tip Switch off the solder station or unplug the solder iron from the station when not in use Replace the...

Page 43: ...wire can be purchased in different diameters For this application it is advisable to use a smaller diameter 1 mm also depending on the diameter of the GND REF wire The soldering time and temperature s...

Page 44: ...gure 45 Soldered wire to solder pad without hole Always inspect the quality of the solder joint under a microscope before implanting Also check the components surrounding the solder pads for eventual...

Page 45: ...nt mat which is connected to earth ground via an ESD compliant cable If continuous grounding of the animal is not feasible the following guidelines should be followed Grounding of the operator via ESD...

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