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[ENH] microelectrode electrophysiology specification (BEP032) #1705

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[ENH] microelectrode electrophysiology specification (BEP032) #1705

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7ec5d5e
Add first BEP032 objects
JuliaSprenger Nov 9, 2022
2f393ca
Add ephys modality, start adding _channels but ran into a question on…
yarikoptic Feb 14, 2024
648781a
Add _acq- to ephys, add _channels and _coords
yarikoptic Mar 6, 2024
d3c9996
Draft for probes TSV file
TheChymera Mar 6, 2024
08c92cd
Fix preferably typo
yarikoptic Mar 15, 2024
e2030ac
Comment out not yet defined iephys and add ephys to datatypes where i…
TheChymera Apr 17, 2024
53f1087
Added probes file
TheChymera Apr 17, 2024
fa648fe
Describe modality/datatype as "Microelectrode Electrophysiology"
yarikoptic Apr 18, 2024
eef67df
Remove iephys entirely since I think it was just inspired by DANDI la…
yarikoptic Apr 18, 2024
27547f9
Initial content for ephys document and initial filename template tree
yarikoptic Apr 18, 2024
a6ae5e2
Merge remote-tracking branch 'upstream/master' into bep032
Remi-Gau Apr 19, 2024
9a20e4b
pacify pre-commit
Remi-Gau Apr 19, 2024
7609276
add to TOC
Remi-Gau Apr 19, 2024
9be41f9
semantic line break and fix
Remi-Gau Apr 19, 2024
983975a
Addressed minor left over lint complains
yarikoptic Apr 19, 2024
1afdc40
Add "Microelectrode" specialization for Electrophysiology in the cont…
yarikoptic Apr 19, 2024
6b39d64
Fix up for bad latin and adjust wording a bit
yarikoptic Apr 19, 2024
f08b163
Replace fancy unicode “ with simple " .
yarikoptic Apr 19, 2024
73012b3
Use redirected to www.datalad.org and www.nwb.org website URLs and fe…
yarikoptic Apr 19, 2024
a46e439
BEP032: ephys -> microephys with {icephys, ecephys} modalities/suffix…
yarikoptic Jun 5, 2024
05e9611
Clarify wording and do mention `microephys` as shorthand for Microele…
yarikoptic Oct 16, 2024
7ddeb75
Adding markdown portion of the Bep032 (#1960)
Peyman-N Nov 20, 2024
2b9e757
[ENH] Schema changes related to BEP032 (#1826)
ree-gupta Nov 20, 2024
6b11f54
Merge remote-tracking branch 'origin/master' into bep032
yarikoptic Nov 20, 2024
1abebea
Some fixes of formatting and URLs
yarikoptic Dec 17, 2024
2a3757d
Merge remote-tracking branch 'origin/master' into bep032
yarikoptic Dec 18, 2024
3f4e941
Adjusted some formatting and some wording at the beginning of the sec…
yarikoptic Dec 18, 2024
0853f8a
Few fixes to the schema from review
yarikoptic Dec 18, 2024
800ba58
Adopting the markdown line lengths for BEP032 (#2012)
Peyman-N Dec 18, 2024
46c91b0
Fix tabulation in a .tsv + convert to use yaw, pitch, roll
yarikoptic Dec 18, 2024
a884604
Add types and min/max for roll,pitch,yaw + fix typo for microephysCha…
yarikoptic Dec 19, 2024
262d5b1
Replace Pharmaceuticals with already existing fields and fix few more…
yarikoptic Dec 19, 2024
756c07c
Merge remote-tracking branch 'origin/master' into bep032
yarikoptic Dec 19, 2024
7bc17cc
Make use of merged fancing for tsvs and add a note about spotted Phar…
yarikoptic Dec 19, 2024
d5fef1f
Remove some "bad latin"
yarikoptic Dec 19, 2024
039fbb3
Fix a link to be final, before redirects
yarikoptic Dec 19, 2024
8e65a63
using MACROS___make_sidecar_table
Peyman-N Jan 17, 2025
2e3be31
numbering
Peyman-N Jan 17, 2025
1762f6f
Adding icephys and ecephys to filename template
Peyman-N Jan 22, 2025
1229a4a
Merge pull request #2034 from Peyman-N/bep032-peyman
yarikoptic Jan 22, 2025
04c1b93
[ENH] Added microephys tag to electrode related enums
ree-gupta Jan 28, 2025
1fd8139
[ENH] Added additional channel enums for microphys
ree-gupta Jan 28, 2025
94de4e5
[ENH] Enlisted microphys channel types in type__channels
ree-gupta Jan 28, 2025
5bc95b0
Merge pull request #2038 from ree-gupta/bep032
yarikoptic Feb 5, 2025
b171eee
Various small fixes from code-review
yarikoptic Feb 6, 2025
73083d8
[BEP032] Moved coord system related entities to correct yaml
ree-gupta Feb 19, 2025
50a38db
Minor tuneups from code review (mostly on wording)
yarikoptic Feb 19, 2025
73976f1
A pass to harmonize to use "microephys" in favor over "ephys"
yarikoptic Feb 19, 2025
387b924
Encode in schema that ATM we do require _electodes and _probes
yarikoptic Feb 19, 2025
d791dc5
One more ephys -> microephys
yarikoptic Feb 19, 2025
41dfec7
Add .json to data (nwb and nix) and _probes files
yarikoptic Feb 19, 2025
cf7e0c6
Merge remote-tracking branch 'origin/master' into bep032
yarikoptic Mar 19, 2025
1242dcd
[DATALAD RUNCMD] replace fancy unicode double quote with a simpler one
yarikoptic Mar 19, 2025
6360b9e
Address many remark lint issues using
yarikoptic Mar 19, 2025
187e6a0
One more tune up
yarikoptic Mar 19, 2025
7b00a28
items
yarikoptic Mar 19, 2025
7954586
[DATALAD RUNCMD] Fix up itemized things indentation
yarikoptic Mar 19, 2025
8ad8a97
Address leftover of remark lint warnings
yarikoptic Mar 19, 2025
4a2a4b4
Merge branch 'bids-standard:bep032' into bep032
ree-gupta Apr 16, 2025
3467824
Remove custom paragraph on participants, replaced angles with yaw, pi…
yarikoptic Apr 16, 2025
fae456f
Merge branch 'master' into bep032
bendichter May 21, 2025
54f8180
Merge branch 'master' into bep032
CodyCBakerPhD Jun 5, 2025
05fcf7d
Merge branch 'master' into bep032
CodyCBakerPhD Jun 12, 2025
fafe10d
[FIX] BEP032 - Correcting validations against real data example (#2132)
CodyCBakerPhD Jun 17, 2025
19845a7
Merge branch 'master' into bep032
CodyCBakerPhD Jun 18, 2025
660317c
Merge branch 'master' into bep032
CodyCBakerPhD Jul 2, 2025
6201738
fix: validation rules for events
CodyCBakerPhD Jul 2, 2025
75787ed
doc: Reorder required metadata files for microephys sessions and clar…
bendichter Jul 2, 2025
d71247c
remove unneeded fields
CodyCBakerPhD Jul 2, 2025
49138dc
move to task.yaml with __
CodyCBakerPhD Jul 2, 2025
2cea859
remove from microephys
CodyCBakerPhD Jul 2, 2025
53ad87b
Update src/modality-specific-files/microelectrode-electrophysiology.md
bendichter Jul 3, 2025
9ca3066
Merge pull request #2153 from bids-standard/bens-reorg
bendichter Jul 3, 2025
937f9f5
Merge branch 'bep032' into fix_rules_bep032
CodyCBakerPhD Jul 11, 2025
62994c7
Merge pull request #2152 from bids-standard/fix_rules_bep032
CodyCBakerPhD Jul 11, 2025
3307e6c
chore: linting
CodyCBakerPhD Jul 30, 2025
28a6199
Merge branch 'bids-standard:bep032' into bep032
ree-gupta Jul 30, 2025
afbdaed
Merge branch 'master' into bep032
bendichter Aug 3, 2025
477719c
Add comprehensive stereotaxic coordinate documentation with visual gu…
bendichter Aug 3, 2025
d3c3d24
Merge branch 'bep032' into bep32_rotation
bendichter Aug 3, 2025
530b22f
Add probe position columns for AP and ML axes and standardize units
bendichter Aug 3, 2025
65ff204
Merge branch 'bep32_rotation' of https://github.com/bids-standard/bid…
bendichter Aug 3, 2025
6f533a6
Update microelectrode electrophysiology documentation
bendichter Aug 3, 2025
b59f0b2
Merge branch 'bep032' into bep32_rotation
bendichter Aug 3, 2025
18ad16b
Merge pull request #2160 from bids-standard/bep32_rotation
bendichter Aug 4, 2025
526c6c6
Merge branch 'bids-standard:bep032' into bep032
ree-gupta Aug 6, 2025
18ce69f
Updated probe tabular rule to match AP, ML, DV
ree-gupta Aug 6, 2025
d4190e6
Removed coordystem completely
ree-gupta Aug 6, 2025
4e44e0a
Removes coordsys macro to fix failing mkdocs build
ree-gupta Aug 6, 2025
c5e2183
change the electrode positions back from AP/ML/DV to x,y,z
bendichter Aug 6, 2025
c921f9b
Update _probes.tsv example with standardized coordinate system and Pr…
bendichter Aug 6, 2025
1dff1da
Merge pull request #2058 from ree-gupta/bep032
ree-gupta Aug 7, 2025
c342954
Merge branch 'master' into bep032
CodyCBakerPhD Aug 13, 2025
ef188c8
Update microephys entity rules and remove task/run requirements
ree-gupta Sep 3, 2025
7f7bac3
Merge branch 'bids-standard:bep032' into bep032
ree-gupta Sep 3, 2025
8485367
Fix linter issues
ree-gupta Sep 3, 2025
068fdc0
Reorganized to match other modalities
ree-gupta Sep 3, 2025
24223af
Merge pull request #2194 from ree-gupta/bep032
ree-gupta Sep 3, 2025
d05b4a6
Clarify DV axis description in microelectrode electrophysiology docum…
bendichter Sep 3, 2025
80e9119
Update src/modality-specific-files/microelectrode-electrophysiology.md
effigies Sep 3, 2025
649a2ce
Adds space entity for microephys electrodes
ree-gupta Sep 4, 2025
b84bd49
Add coordinate system metadata fields for microephys
ree-gupta Sep 4, 2025
cfd64cc
Added rules to 1) override rule for coorsystem to be present for elec…
ree-gupta Sep 4, 2025
198e365
Added entities for the photo specific to microephys
ree-gupta Sep 4, 2025
cf3e7a9
Rewrote the coordsystem JSON and photo section to align with ieeg but…
ree-gupta Sep 4, 2025
2f3069f
Minor change to the default probe relative coordinate system
ree-gupta Sep 4, 2025
4395dcf
Probe interface exaple file tree
ree-gupta Sep 4, 2025
e295e74
Resolve merge conflict due to reorganization of events from task.yaml…
ree-gupta Sep 4, 2025
f3640c0
Merge branch 'master' into bep032
CodyCBakerPhD Sep 17, 2025
dada00c
Merge pull request #2198 from ree-gupta/bep032
ree-gupta Sep 17, 2025
c272e01
Merge branch 'master' into bep032
CodyCBakerPhD Sep 19, 2025
c31f579
Add omission of microephys datatypes for overall channel file rule
ree-gupta Oct 1, 2025
d7437f5
Merge branch 'master' into bep032
bendichter Oct 1, 2025
101c01a
Update src/modality-specific-files/microelectrode-electrophysiology.md
bendichter Oct 1, 2025
55401ec
Merge branch 'bep032' into bep032
ree-gupta Oct 1, 2025
84f44f1
Merge pull request #2224 from ree-gupta/bep032
ree-gupta Oct 1, 2025
54a44d4
Update src/modality-specific-files/microelectrode-electrophysiology.md
bendichter Oct 1, 2025
6a9cf98
Update src/modality-specific-files/microelectrode-electrophysiology.md
bendichter Oct 1, 2025
47cca5f
Fix indentation for note and example alerts
yarikoptic Oct 1, 2025
e049ef9
Merge branch 'master' into bep032
bendichter Oct 7, 2025
59e1267
[MISC] Use Levels and custom json for probe interface files
bendichter Oct 7, 2025
94b09d8
Update src/modality-specific-files/microelectrode-electrophysiology.md
bendichter Oct 7, 2025
45a06b7
Update src/schema/objects/columns.yaml
bendichter Oct 7, 2025
89fa748
Update src/modality-specific-files/microelectrode-electrophysiology.md
bendichter Oct 7, 2025
551f5de
[MISC] Replace image syntax with HTML for anatomical reference diagrams
bendichter Oct 7, 2025
40e7a5d
Merge branch 'bep032' of https://github.com/bids-standard/bids-specif…
bendichter Oct 7, 2025
cc7fe98
Fix formatting in example *_electrodes.tsv for improved readability
bendichter Oct 7, 2025
ad41192
Apply suggestion from @bendichter
bendichter Oct 7, 2025
da05a28
Remove channel_id def and use name__channels same as ieeg
ree-gupta Oct 14, 2025
d9266b7
Update microephys electrode.tsv to match ieeg
ree-gupta Oct 14, 2025
4fc8ec8
Changed probe_id to probe_name to avoid use of the concept ID against…
ree-gupta Oct 14, 2025
8a933ec
Merge branch 'bids-standard:bep032' into bep032
ree-gupta Oct 14, 2025
79f1059
Add missing probe_height def and rewrite desc to match current markdown
ree-gupta Oct 14, 2025
40993d2
Fixed minor typo failing schema validation
ree-gupta Oct 14, 2025
41b301d
Fix remark linting issues
ree-gupta Oct 14, 2025
4c95199
Added and modified texts for coordsystem requirements
ree-gupta Oct 14, 2025
05d19bf
Added icephys and ecephys distinction and restructured first section …
ree-gupta Oct 14, 2025
a127f57
Fixed initial_column to match AP, ML, DV
ree-gupta Oct 14, 2025
4c776e5
Update mock TSV and JSON and fix heading levels to match ieeg
ree-gupta Oct 14, 2025
d428dc8
Updated toy data section and links to example to match current spec
ree-gupta Oct 14, 2025
73d3975
Minor formatting and style issues
ree-gupta Oct 14, 2025
7fb3a28
Fix mock data tsv and JSON
ree-gupta Oct 15, 2025
8b39a2d
Merge branch 'master' into bep032
CodyCBakerPhD Oct 15, 2025
1cfa706
Apply various wording suggestions from code review
yarikoptic Oct 17, 2025
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1 change: 1 addition & 0 deletions mkdocs.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@ nav:
- Near-Infrared Spectroscopy: modality-specific-files/near-infrared-spectroscopy.md
- Motion: modality-specific-files/motion.md
- Magnetic Resonance Spectroscopy: modality-specific-files/magnetic-resonance-spectroscopy.md
- Microelectrode Electrophysiology: modality-specific-files/microelectrode-electrophysiology.md
- Derivatives:
- BIDS Derivatives: derivatives/introduction.md
- Common data types and metadata: derivatives/common-data-types.md
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672 changes: 672 additions & 0 deletions src/modality-specific-files/microelectrode-electrophysiology.md
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