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SpikeGLX

What

SpikeGLX is a recording system for extracellular neural probes. The emphasis is on concurrent synchronous recording from high channel count probes together with numerous auxiliary analog and digital channels:

  • Concurrent, synchronized acquisition from Imec probes, OneBoxes and NI-DAQ devices.
  • Supports all Neuropixels probe generations and types.
  • Supports HHMI/Whisper system.
  • Integration with live anatomical tracking: Pinpoint; Trajectory Explorer.
  • Flexible visualization, filtering and sorting tools.
  • Programmable triggering.
  • Remote control and extensibility via MATLAB, C++, C, C#, Python.
  • Powerful offline viewing and editing.

Imec Project Phases

There are five branches in this repo separately supporting the five Imec Neuropixels project development phases. The five phases have mutually incompatible hardware and software, so obtain the appropriate materials for your needs. Release software packages are labeled as phase3A, phase3B1, phase3B2, phase20, or phase30. All early releases having no phase label are actually phase3A. All releases support NI-DAQ based acquisition.

  • Phase3A: Initially, 4 flavors of prototype probe (option 1, 2, 3, 4) were created enabling consortium members to choose the most useful architecture and feature set. Phase3A probes are connected one at a time to a Xilinx Kintex 7 FPGA board, and accessed via Ethernet. The probes, cables, HS and BSC parts are specific to phase3A.

  • Phase3B1: At this phase, option 3 probes had won and were further developed for commercial production. The same Xilinx board is retained for one at a time probe operation over Ethernet (but reprogrammed for 3B1). The cables, HS and BSC parts are all specific to 3B1. The 3B probes can be run with either 3B1 or 3B2 setups.

  • Phase3B2: A.k.a. Neuropixels 1.0. This phase replaces the Xilinx board with PXIe based modules, each of which connects up to 4 probes. Several modules can be operated together from one PXI chassis and one application. The probes are the same as phase3B1, but all other hardware parts are specific to the PXIe implementation.

  • Phase20: A.k.a. Neuropixels 2.0, introduces specific probes and HS with a more compact design. The HS each support two probes. The same PXIe modules can be used with a firmware update. SpikeGLX for this phase is specific to 2.0 hardware.

  • Phase30: This is unified software to support Neuropixels 1.0, 2.0 and all other probe hardware going forward. Again, the same base station modules can be used after updating their firmware, which can be done via SpikeGLX.

Who

SpikeGLX is developed by Bill Karsh of the Tim Harris Lab at HHMI/Janelia Research Campus.

Based on the SpikeGL extracellular data acquisition system originally developed by Calin A. Culianu.

Compiled Software

Official release software and support materials are here: SpikeGLX Download Page.

System Requirements

Requirements differ according to platform:

Help

If there is any problem with the slack channel invitation, email the administrator.

Frequently Asked Questions

SpikeGLX FAQ.

Licensing

Use is subject to Janelia Research Campus Software Copyright 1.2 license terms: http://license.janelia.org/license.

QLed components are subject to GNU Library GPL v2.0 terms, which are described here: QLed-LGPLv2-LICENSE.txt.

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