Julia Sprenger fab82ad00d gin commit from nit-ope-de04 il y a 2 ans
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CatGT fab82ad00d gin commit from nit-ope-de04 il y a 2 ans
SpikeGLX fab82ad00d gin commit from nit-ope-de04 il y a 2 ans
README.md 39267a04da gin commit from nit-ope-de04 il y a 2 ans

README.md

Recording date: 5-19-2022 Contact: Graham Findlay (gfindlay@wisc.edu) Probes: 2x Neuropixel 1.0 submerged in ACSF. SpikeGLX version: v.20201103

Every SpikeGLX run consists of 2 probes (imec0 & imec1) x 2 cycles (g0 & g1) x 2 t-files (t0 & t1).

SpikeGLX Runs

  • 5-19-2022-CI0
    • t-files are continuous: 10ms each, with a 0s inter-file interval.
    • Folder-per-probe organization.
  • 5-19-2022-CI1
    • t-files are continuous: 10ms each, with a 0s inter-file interval.
    • Single-folder organization.
  • 5-19-2022-CI2
    • t-files are discontinuous: 10ms each with a 1s inter-file interval.
    • Folder-per-probe organization.
  • 5-19-2022-CI3
    • t-files are discontinuous: 10ms each with a 1s inter-file interval.
    • Single-folder organization.
  • 5-19-2022-CI4
    • t-files are overlapping: 20ms each with 10ms overlap.
    • Folder-per-probe organization.
  • 5-19-2022-CI4
    • t-files are overlapping: 20ms each with 10ms overlap.
    • Single-folder organization.

CatGT-processed files

  • CatGT-A
    • This is a concatenation of both t-files from the first cycle ONLY (i.e. _g0_t0 + g0_t1) of 5-19-2022-CI0. The output uses folder-per-probe organization.
    • Cmdline: CatGT -dir=/path/to/5-19-2022-CI0 -run=5-19-2022-CI0 -g=0 -t=0,1 -prb_fld -ap -lf -prb=0:1 -no_auto_sync -zerofillmax=0 -dest=/path/to/CatGT-A -out_prb_fld
  • CatGT-B
    • Like CatGT-A, this is a concatenation of both t-files from the first cycle ONLY of 5-19-2022-CI0, but the output uses single-folder organization.
    • Cmdline: CatGT -dir=/path/to/5-19-2022-CI0 -run=5-19-2022-CI0 -g=0 -t=0,1 -prb_fld -ap -lf -prb=0:1 -no_auto_sync -zerofillmax=0 -dest=/path/to/CatGT-B
  • CatGT-C
    • This is a concatenation of both t-files from BOTH cycles (i.e. _g0_t0 + g0_t1 + g1_t0 + g1_t1) of 5-19-2022-CI0. The output uses folder-per-probe organization.
    • Cmdline: CatGT -dir=/path/to/5-19-2022-CI0 -run=5-19-2022-CI0 -g=0,1 -t=0,1 -prb_fld -ap -lf -prb=0:1 -no_auto_sync -zerofillmax=0 -dest=/path/to/CatGT-C -out_prb_fld
  • CatGT-D
    • Like CatGT-C, this is a concatenation of both t-files from BOTH cycles of 5-19-2022-CI0, but the output uses single-folder organization.
    • Cmdline: CatGT -dir=/path/to/5-19-2022-CI0 -run=5-19-2022-CI0 -g=0,1 -t=0,1 -prb_fld -ap -lf -prb=0:1 -no_auto_sync -zerofillmax=0 -dest=/path/to/CatGT-D
  • CatGT-E
    • This is a concatenation of both t-files from both cycles of 5-19-2022-CI2. The output uses folder-per-probe organization.
    • Cmdline: CatGT -dir=/path/to/5-19-2022-CI2 -run=5-19-2022-CI2 -g=0,1 -t=0,1 -prb_fld -ap -lf -prb=0:1 -no_auto_sync -zerofillmax=0 -dest=/path/to/CatGT-E -out_prb_fld
  • Supercat-A
    • This is a concatenation of CatGT-A and CatGT-E. The output uses folder-per-probe organization.
    • Cmdline: CatGT -prb_fld -ap -lf -prb=0:1 -no_auto_sync -supercat={/path/to/CatGT-A,catgt_5-19-2022-CI0_g0}{/path/to/CatGT-E,catgt_5-19-2022-CI2_g0} -dest=/path/to/Supercat-A -out_prb_fld

Notes on CatGT options used:

  • CatGT normally preserves the real-world duration of the recording by zero-filling gaps between t-files. In order to keep file sizes here as small as possible, we use zerofillmax=0 to prevent this behavior.
  • Files are so short that they include no sync edges, and I use a custom sync scheme anyways. So files are processed with -no_auto_sync.
datacite.yml
Title Electrophysiology Testing Data
Authors Sprenger,Julia;Institut de Neurosciences de La Timone, CNRS & Aix-Marseille University, Marseille, France;ORCID:0000-0002-9986-7477
Garcia,Samuel;Centre de Recherche en Neuroscience de Lyon, CNRS, Lyon, France;ORCID:0000-0001-6389-9779
Description Collection of testing data in various electrophysiology file formats.
License Open Data Commons Open Database License (ODbL) (https://opendatacommons.org/licenses/odbl/1.0/)
References Neo (RRID:SCR_000634) [RRID:SCR_000634] (IsSupplementTo)
SpikeInterface (RRID:SCR_021150) [RRID:SCR_021150] (IsSupplementTo)
Funding
Keywords Neuroscience
File Format
Test Data
Resource Type Dataset