Concurrent, synchronized acquisition from Imec and NI-DAQ devices.
Topics:
There are four branches in this repo separately supporting the four Imec Neuropixels project development phases. The four phases have mutually incompatible hardware and software, so obtain the appropriate materials for your needs. Release software packages are labeled as phase3A, phase3B1, phase3B2, or phase20. 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: 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 the phase3B1, but all other hardware parts are specific to the PXIe implementation.
Phase20: 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. Initially, SpikeGLX for this phase is specific to 2.0 hardware. In future one app will run 2.0 and 3B2 hardware.
Requirements differ according to platform:
Suggested organization: Create folder 'SpikeGLX' on your desktop or
C:\then download/unzip associated stuff into it:
SpikeGLX\
Release_v20190919-phase20.zip
Release_v20190413-phase3B2.zip
Release_v20190919-phase20\
Release_v20190413-phase3B2\
Drivers\
Enclustra_Windows_10\
Tools\
Etc\Release 20190214-phase3B2...Readme : First PXI, Imec v1.15
Release 20180325-phase3B1...Readme : Fixed-up 3B1, Imec v5.1
Release 20171101-phase3A...Readme : Synchronization, Imec v4.3
These required driver files are not included in your SpikeGLX release.
Terminology: 'Enclustra' is a company that markets other vendor's FPGAs along with development and support tools. There are several FPGAs used in the Neuropixels hardware, including a Xilinx Zynq model, often referred to as 'the enclustra'.
Descriptions of metafile items for each phase:
MATLAB and Python tools for parsing meta and binary datafiles (supports 3A, 3B1, 3B2, 20).
CatGT is a command-line tool that does the following offline operations (all imec phases):
- Join trials with given run_name and g-index in t-index range [ta,tb]...
- ...Or run on any individual file.
- Optionally apply bandpass and global demux CAR filters.
- Optionally edit out saturation artifacts.
- Optionally extract tables of TTL event times.
- CatGT: Global Demuxed CAR
TPrime is a command line tool that maps event times (all imec phases):
- Map time from one SpikeGLX data stream to any other.
- Translate all events to a single common timeline.
- Uses sync edges to achieve 1 to 2 sample accuracy.
- Maps TTL events extracted using CatGT.
- Maps spike times from any sorter.
- Sync: Aligning with Edges.
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: https://github.com/billkarsh/SpikeGLX/blob/master/QLed-LGPLv2-LICENSE.txt.
fin