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7ec5d5e
Add first BEP032 objects
Nov 9, 2022
2f393ca
Add ephys modality, start adding _channels but ran into a question on…
Feb 14, 2024
648781a
Add _acq- to ephys, add _channels and _coords
Mar 6, 2024
d3c9996
Draft for probes TSV file
Mar 6, 2024
08c92cd
Fix preferably typo
Mar 15, 2024
e2030ac
Comment out not yet defined iephys and add ephys to datatypes where i…
Apr 17, 2024
53f1087
Added probes file
Apr 17, 2024
fa648fe
Describe modality/datatype as "Microelectrode Electrophysiology"
Apr 18, 2024
eef67df
Remove iephys entirely since I think it was just inspired by DANDI la…
Apr 18, 2024
27547f9
Initial content for ephys document and initial filename template tree
Apr 18, 2024
a6ae5e2
Merge remote-tracking branch 'upstream/master' into bep032
Apr 19, 2024
9a20e4b
pacify pre-commit
Apr 19, 2024
7609276
add to TOC
Apr 19, 2024
9be41f9
semantic line break and fix
Apr 19, 2024
983975a
Addressed minor left over lint complains
Apr 19, 2024
1afdc40
Add "Microelectrode" specialization for Electrophysiology in the cont…
Apr 19, 2024
6b39d64
Fix up for bad latin and adjust wording a bit
Apr 19, 2024
f08b163
Replace fancy unicode “ with simple " .
Apr 19, 2024
73012b3
Use redirected to www.datalad.org and www.nwb.org website URLs and fe…
Apr 19, 2024
a46e439
BEP032: ephys -> microephys with {icephys, ecephys} modalities/suffix…
Jun 5, 2024
05e9611
Clarify wording and do mention `microephys` as shorthand for Microele…
Oct 16, 2024
7ddeb75
Adding markdown portion of the Bep032 (#1960)
Nov 20, 2024
2b9e757
[ENH] Schema changes related to BEP032 (#1826)
Nov 20, 2024
6b11f54
Merge remote-tracking branch 'origin/master' into bep032
Nov 20, 2024
1abebea
Some fixes of formatting and URLs
Dec 17, 2024
2a3757d
Merge remote-tracking branch 'origin/master' into bep032
Dec 18, 2024
3f4e941
Adjusted some formatting and some wording at the beginning of the sec…
Dec 18, 2024
0853f8a
Few fixes to the schema from review
Dec 18, 2024
800ba58
Adopting the markdown line lengths for BEP032 (#2012)
Dec 18, 2024
46c91b0
Fix tabulation in a .tsv + convert to use yaw, pitch, roll
Dec 18, 2024
a884604
Add types and min/max for roll,pitch,yaw + fix typo for microephysCha…
Dec 19, 2024
262d5b1
Replace Pharmaceuticals with already existing fields and fix few more…
Dec 19, 2024
756c07c
Merge remote-tracking branch 'origin/master' into bep032
Dec 19, 2024
7bc17cc
Make use of merged fancing for tsvs and add a note about spotted Phar…
Dec 19, 2024
d5fef1f
Remove some "bad latin"
Dec 19, 2024
039fbb3
Fix a link to be final, before redirects
Dec 19, 2024
8e65a63
using MACROS___make_sidecar_table
Jan 17, 2025
2e3be31
numbering
Jan 17, 2025
1762f6f
Adding icephys and ecephys to filename template
Jan 22, 2025
1229a4a
Merge pull request #2034 from Peyman-N/bep032-peyman
Jan 22, 2025
04c1b93
[ENH] Added microephys tag to electrode related enums
Jan 28, 2025
1fd8139
[ENH] Added additional channel enums for microphys
Jan 28, 2025
94de4e5
[ENH] Enlisted microphys channel types in type__channels
Jan 28, 2025
5bc95b0
Merge pull request #2038 from ree-gupta/bep032
Feb 5, 2025
b171eee
Various small fixes from code-review
Feb 6, 2025
73083d8
[BEP032] Moved coord system related entities to correct yaml
Feb 19, 2025
50a38db
Minor tuneups from code review (mostly on wording)
Feb 19, 2025
73976f1
A pass to harmonize to use "microephys" in favor over "ephys"
Feb 19, 2025
387b924
Encode in schema that ATM we do require _electodes and _probes
Feb 19, 2025
d791dc5
One more ephys -> microephys
Feb 19, 2025
41dfec7
Add .json to data (nwb and nix) and _probes files
Feb 19, 2025
cf7e0c6
Merge remote-tracking branch 'origin/master' into bep032
Mar 19, 2025
1242dcd
[DATALAD RUNCMD] replace fancy unicode double quote with a simpler one
Mar 19, 2025
6360b9e
Address many remark lint issues using
Mar 19, 2025
187e6a0
One more tune up
Mar 19, 2025
7b00a28
items
Mar 19, 2025
7954586
[DATALAD RUNCMD] Fix up itemized things indentation
Mar 19, 2025
8ad8a97
Address leftover of remark lint warnings
Mar 19, 2025
4a2a4b4
Merge branch 'bids-standard:bep032' into bep032
Apr 16, 2025
3467824
Remove custom paragraph on participants, replaced angles with yaw, pi…
Apr 16, 2025
fae456f
Merge branch 'master' into bep032
May 21, 2025
54f8180
Merge branch 'master' into bep032
Jun 5, 2025
05fcf7d
Merge branch 'master' into bep032
Jun 12, 2025
fafe10d
[FIX] BEP032 - Correcting validations against real data example (#2132)
Jun 17, 2025
19845a7
Merge branch 'master' into bep032
Jun 18, 2025
660317c
Merge branch 'master' into bep032
Jul 2, 2025
6201738
fix: validation rules for events
Jul 2, 2025
75787ed
doc: Reorder required metadata files for microephys sessions and clar…
Jul 2, 2025
d71247c
remove unneeded fields
Jul 2, 2025
49138dc
move to task.yaml with __
Jul 2, 2025
2cea859
remove from microephys
Jul 2, 2025
53ad87b
Update src/modality-specific-files/microelectrode-electrophysiology.md
Jul 3, 2025
9ca3066
Merge pull request #2153 from bids-standard/bens-reorg
Jul 3, 2025
937f9f5
Merge branch 'bep032' into fix_rules_bep032
Jul 11, 2025
62994c7
Merge pull request #2152 from bids-standard/fix_rules_bep032
Jul 11, 2025
3307e6c
chore: linting
Jul 30, 2025
28a6199
Merge branch 'bids-standard:bep032' into bep032
Jul 30, 2025
afbdaed
Merge branch 'master' into bep032
Aug 3, 2025
477719c
Add comprehensive stereotaxic coordinate documentation with visual gu…
Aug 3, 2025
d3c3d24
Merge branch 'bep032' into bep32_rotation
Aug 3, 2025
530b22f
Add probe position columns for AP and ML axes and standardize units
Aug 3, 2025
65ff204
Merge branch 'bep32_rotation' of https://github.com/bids-standard/bid…
Aug 3, 2025
6f533a6
Update microelectrode electrophysiology documentation
Aug 3, 2025
b59f0b2
Merge branch 'bep032' into bep32_rotation
Aug 3, 2025
18ad16b
Merge pull request #2160 from bids-standard/bep32_rotation
Aug 4, 2025
526c6c6
Merge branch 'bids-standard:bep032' into bep032
Aug 6, 2025
18ce69f
Updated probe tabular rule to match AP, ML, DV
Aug 6, 2025
d4190e6
Removed coordystem completely
Aug 6, 2025
4e44e0a
Removes coordsys macro to fix failing mkdocs build
Aug 6, 2025
c5e2183
change the electrode positions back from AP/ML/DV to x,y,z
Aug 6, 2025
c921f9b
Update _probes.tsv example with standardized coordinate system and Pr…
Aug 6, 2025
1dff1da
Merge pull request #2058 from ree-gupta/bep032
Aug 7, 2025
c342954
Merge branch 'master' into bep032
Aug 13, 2025
ef188c8
Update microephys entity rules and remove task/run requirements
Sep 3, 2025
7f7bac3
Merge branch 'bids-standard:bep032' into bep032
Sep 3, 2025
8485367
Fix linter issues
Sep 3, 2025
068fdc0
Reorganized to match other modalities
Sep 3, 2025
24223af
Merge pull request #2194 from ree-gupta/bep032
Sep 3, 2025
d05b4a6
Clarify DV axis description in microelectrode electrophysiology docum…
Sep 3, 2025
80e9119
Update src/modality-specific-files/microelectrode-electrophysiology.md
Sep 3, 2025
649a2ce
Adds space entity for microephys electrodes
Sep 4, 2025
b84bd49
Add coordinate system metadata fields for microephys
Sep 4, 2025
cfd64cc
Added rules to 1) override rule for coorsystem to be present for elec…
Sep 4, 2025
198e365
Added entities for the photo specific to microephys
Sep 4, 2025
cf3e7a9
Rewrote the coordsystem JSON and photo section to align with ieeg but…
Sep 4, 2025
2f3069f
Minor change to the default probe relative coordinate system
Sep 4, 2025
4395dcf
Probe interface exaple file tree
Sep 4, 2025
e295e74
Resolve merge conflict due to reorganization of events from task.yaml…
Sep 4, 2025
f3640c0
Merge branch 'master' into bep032
Sep 17, 2025
dada00c
Merge pull request #2198 from ree-gupta/bep032
Sep 17, 2025
c272e01
Merge branch 'master' into bep032
Sep 19, 2025
c31f579
Add omission of microephys datatypes for overall channel file rule
Oct 1, 2025
d7437f5
Merge branch 'master' into bep032
Oct 1, 2025
101c01a
Update src/modality-specific-files/microelectrode-electrophysiology.md
Oct 1, 2025
55401ec
Merge branch 'bep032' into bep032
Oct 1, 2025
84f44f1
Merge pull request #2224 from ree-gupta/bep032
Oct 1, 2025
54a44d4
Update src/modality-specific-files/microelectrode-electrophysiology.md
Oct 1, 2025
6a9cf98
Update src/modality-specific-files/microelectrode-electrophysiology.md
Oct 1, 2025
47cca5f
Fix indentation for note and example alerts
Oct 1, 2025
e049ef9
Merge branch 'master' into bep032
Oct 7, 2025
59e1267
[MISC] Use Levels and custom json for probe interface files
Oct 7, 2025
94b09d8
Update src/modality-specific-files/microelectrode-electrophysiology.md
Oct 7, 2025
45a06b7
Update src/schema/objects/columns.yaml
Oct 7, 2025
89fa748
Update src/modality-specific-files/microelectrode-electrophysiology.md
Oct 7, 2025
551f5de
[MISC] Replace image syntax with HTML for anatomical reference diagrams
Oct 7, 2025
40e7a5d
Merge branch 'bep032' of https://github.com/bids-standard/bids-specif…
Oct 7, 2025
cc7fe98
Fix formatting in example *_electrodes.tsv for improved readability
Oct 7, 2025
ad41192
Apply suggestion from @bendichter
Oct 7, 2025
da05a28
Remove channel_id def and use name__channels same as ieeg
Oct 14, 2025
d9266b7
Update microephys electrode.tsv to match ieeg
Oct 14, 2025
4fc8ec8
Changed probe_id to probe_name to avoid use of the concept ID against…
Oct 14, 2025
8a933ec
Merge branch 'bids-standard:bep032' into bep032
Oct 14, 2025
79f1059
Add missing probe_height def and rewrite desc to match current markdown
Oct 14, 2025
40993d2
Fixed minor typo failing schema validation
Oct 14, 2025
41b301d
Fix remark linting issues
Oct 14, 2025
4c95199
Added and modified texts for coordsystem requirements
Oct 14, 2025
05d19bf
Added icephys and ecephys distinction and restructured first section …
Oct 14, 2025
a127f57
Fixed initial_column to match AP, ML, DV
Oct 14, 2025
4c776e5
Update mock TSV and JSON and fix heading levels to match ieeg
Oct 14, 2025
d428dc8
Updated toy data section and links to example to match current spec
Oct 14, 2025
73d3975
Minor formatting and style issues
Oct 14, 2025
7fb3a28
Fix mock data tsv and JSON
Oct 15, 2025
8b39a2d
Merge branch 'master' into bep032
Oct 15, 2025
1cfa706
Apply various wording suggestions from code review
Oct 17, 2025
ae05b3b
Apply suggestion from @yarikoptic
Oct 26, 2025
d1835cf
Apply suggestion from @bendichter
Oct 26, 2025
76ef60a
add back type info that was accidentally removed from whole_blood_rad…
Oct 26, 2025
8368d47
Update link to iEEG stimulation documentation for clarity
Oct 26, 2025
401ee96
Merge branch 'master' into bep032
Nov 5, 2025
df637a4
Update src/modality-specific-files/microelectrode-electrophysiology.md
Nov 5, 2025
e970799
feat: add anatomical reference point to microelectrode electrophysiol…
Nov 5, 2025
91e4cb8
Fix up units and clarify that we need TODO work on the units/space more
Nov 5, 2025
e14db80
Fix typo Update src/schema/objects/suffixes.yaml
Nov 21, 2025
cd7e17e
Merge branch 'master' into bep032
Dec 3, 2025
624ea76
rf: move "ProbeInterface Library" subsection down after probes.tsv
Dec 3, 2025
6499d0c
Revert "Apply suggestion from @bendichter" to bring back width__probes
Dec 3, 2025
cd7045e
docs: consolidate electrode coordinate system documentation
Dec 8, 2025
00aa234
docs(appendices): add microelectrode surgical coordinates appendix
Dec 8, 2025
33faf8f
Add probes related schema changes
Dec 8, 2025
97b616e
Merge branch 'master' into bep032
Dec 8, 2025
6284d36
docs: add microelectrode electrophysiology coordinate systems
Dec 8, 2025
724e4a2
Merge branch 'bep032' into bep032-coord-enum
Dec 8, 2025
803cf2c
[pre-commit.ci] auto fixes from pre-commit.com hooks
Dec 8, 2025
a92aad0
docs: convert RRID identifiers to hyperlinks in coordinate-systems
Dec 8, 2025
0957556
Merge pull request #2276 from bids-standard/bep032-coord-enum
Dec 8, 2025
36ab944
docs(ephys): add stream_id column documentation for channels.tsv
Dec 8, 2025
d12bfc1
docs(ephys): clarify electrode name uniqueness requirement
Dec 8, 2025
d6227c6
Merge pull request #2277 from bids-standard/bep032-stream_id
Dec 8, 2025
c162e31
Changed hemisphere cardinality from required to recommended
Dec 10, 2025
10886f9
Merge branch 'master' into bep032
Dec 10, 2025
544307b
fix: correct typo in description for reference__microephys
Dec 10, 2025
ef8a24e
fix: clarify electrode position coordinates for single electrode cases
Dec 10, 2025
70ccf9b
Merge branch 'bep032' into bpe032-electrode-name-uniqueness
Dec 10, 2025
63d7b89
fix: fix the name of matrial: material_probes -> material
Dec 15, 2025
cff172a
fix: remove unnecessary brackets in coordsystem selectors
Dec 15, 2025
0a5a656
fix: change tables from pipe syntax to html syntax. This removes lint…
Dec 15, 2025
0b6489c
Fix yamllint and codespell issues
Dec 17, 2025
b4ce1a1
feat(microephys): add channel-level filtering columns and documentation
Dec 26, 2025
777f533
fix: add missing closing brace in JSON example for task description
Dec 26, 2025
5af6791
fix: update description of MicroephysCoordinateSystem axes and link t…
Dec 26, 2025
1c3a26f
feat(schema): add model column for probes and fix electrode descriptions
Dec 26, 2025
35a64f1
fix: update description for IntendedFor field in microephysCoordsyste…
Dec 26, 2025
61a3372
fix: correct name and type for associated_brain_region_id field in co…
Dec 26, 2025
d1a010b
fix: remove deprecated hardware_filters and software_filters columns …
Dec 26, 2025
29bde4e
feat: add micrometer (um) as a valid unit for MicroephysCoordinateUnits
Dec 26, 2025
a597f3a
fix(schema): correct stereotaxic coordinate system axis definitions
Dec 26, 2025
a557abb
feat(microephys): add recording metadata fields to setup schema
Dec 26, 2025
605e2f5
docs(ephys): correct JSON metadata filename convention
Dec 26, 2025
b258c64
fix: correct pluralization in TODO comment for PharmaceuticalDoseUnits
Dec 26, 2025
9e3423c
fix(schema): update electrode position descriptions for clarity and c…
Dec 26, 2025
2c1e9c5
fix(schema): rename x/y/z columns to x/y/z__electrodes in microephys
Dec 26, 2025
eb5cd05
docs(ephys): update coordinate system names and fix Stereotaxic spelling
Dec 26, 2025
d7f09d7
feat(microephys): add brain atlas coordinate systems for rodents and …
Dec 26, 2025
50b0e73
Merge branch 'master' into bep032
Jan 4, 2026
e70421a
fix(linter): fix yamllint and remark errors
Jan 4, 2026
78719a5
fix(schema): remove unused column defintions
Jan 4, 2026
e88c744
Reverted commit and readded the removed type column for software_filters
Jan 4, 2026
f8217b0
fix: reconciling software_filter defintion with master
Jan 4, 2026
10893e8
Update src/schema/objects/metadata.yaml
Jan 4, 2026
6342c72
Update src/modality-specific-files/microelectrode-electrophysiology.md
Jan 4, 2026
bc2d1dd
Merge branch 'bep032' into bpe032-electrode-name-uniqueness
Jan 4, 2026
fa07b77
Merge pull request #2278 from bids-standard/bpe032-electrode-name-uni…
Jan 4, 2026
38248f1
fix: microephys electrodes/coordsystem validation with space entity s…
Jan 4, 2026
0a0748e
fix(convention): update the schema selector convention from == to usi…
Jan 4, 2026
40cdcdc
fix(convention): use __ instead of _ for microephys context
Jan 4, 2026
5e91f38
cleanup(schema): remove old unused probe suffix
Jan 4, 2026
7a23830
cleanup(schema): remove unsused column contact_count
Jan 4, 2026
7c6aed2
fix(convention): fix display name capitalization and hypenation
Jan 4, 2026
ad50350
[BEP032] Review and clean-up suggestions (#2293)
Jan 6, 2026
5f71366
Update src/modality-specific-files/microelectrode-electrophysiology.md
Jan 7, 2026
87de228
Update src/modality-specific-files/microelectrode-electrophysiology.md
Jan 7, 2026
95ee115
Update src/modality-specific-files/microelectrode-electrophysiology.md
Jan 7, 2026
3b2a8fe
Update src/modality-specific-files/microelectrode-electrophysiology.md
Jan 7, 2026
673d107
Update src/modality-specific-files/microelectrode-electrophysiology.md
Jan 7, 2026
607a042
enh(schema): add electrode_name, make reference optional and generali…
Jan 7, 2026
eb893f3
Remove dimension_unit from electrode table description
Jan 7, 2026
c2978a5
Remove redundant statement about required columns order in *_electrod…
Jan 7, 2026
5e56978
move description of electrode position columns in microelectrode elec…
Jan 7, 2026
b46c11f
cleanup: remove additions to events that are not microephys specific
Jan 7, 2026
659c57c
Remove outdated comments and streamline pharmaceuticals section in mi…
Jan 7, 2026
78478ef
Merge branch 'bep032' of https://github.com/bids-standard/bids-specif…
Jan 7, 2026
6aa3f0e
update source attribution to BrainSTEM
Jan 7, 2026
f72e70b
fix(linter): fix remark linter error
Jan 8, 2026
7cb141f
Merge branch 'master' into bep032
Jan 8, 2026
67821db
fix(build): add missing closing ticks for TSV in md
Jan 8, 2026
7a1d9f1
Update src/modality-specific-files/microelectrode-electrophysiology.md
Jan 8, 2026
f1f472f
Update src/modality-specific-files/microelectrode-electrophysiology.md
Jan 8, 2026
e3ccafd
Merge branch 'master' into bep032
Jan 9, 2026
078ce68
docs(ephys): add electrode_name column to channels table example
Jan 9, 2026
3fde7c4
fix(microephys): move reference__microephys to be optional in channel…
Jan 9, 2026
5cbe907
move reference__microephys
Jan 9, 2026
bec3b0b
fix(coordinate-systems): update link format for Microelectrode Surgic…
Jan 12, 2026
9e465ed
Merge branch 'master' into bep032
Jan 14, 2026
f21acbf
fix: Correct formatting in electrode data table for clarity
Jan 14, 2026
bb009bf
fix: Correct electrode name formatting in electrophysiology examples …
Jan 14, 2026
27adf0e
docs: correct coordinate system descriptions and references
Jan 15, 2026
bbb8e1f
fix: Add ignore rule for SciCrunch URLs in link checker
Jan 15, 2026
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1 change: 1 addition & 0 deletions mkdocs.yml
Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@ 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
Expand Down
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1,010 changes: 1,010 additions & 0 deletions src/modality-specific-files/microelectrode-electrophysiology.md

Large diffs are not rendered by default.

15 changes: 12 additions & 3 deletions src/schema/meta/associations.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -74,7 +74,7 @@ bvec:

channels:
selectors:
- intersects([suffix], ['eeg', 'ieeg', 'meg', 'nirs', 'motion', 'optodes'])
- intersects([suffix], ['eeg', 'ieeg', 'meg', 'nirs', 'motion', 'optodes', 'ecephys', 'icephys'])
- extension != '.json'
target:
suffix: channels
Expand All @@ -83,7 +83,7 @@ channels:

coordsystem:
selectors:
- intersects([suffix], ['eeg', 'ieeg', 'meg', 'nirs', 'motion', 'electrodes', 'optodes'])
- intersects([suffix], ['eeg', 'ieeg', 'meg', 'nirs', 'motion', 'electrodes', 'optodes', 'ecephys', 'icephys']])
- extension != '.json'
target:
suffix: coordsystem
Expand All @@ -92,11 +92,20 @@ coordsystem:

electrodes:
selectors:
- intersects([suffix], ['eeg', 'ieeg', 'meg'])
- intersects([suffix], ['eeg', 'ieeg', 'meg', 'ecephys', 'icephys'])
- extension != '.json'
target:
suffix: electrodes
extension: .tsv
entities:
- space
inherit: true

probes:
selectors:
- intersects([suffix], ['ecephys', 'icephys'])
- extension != '.json'
target:
suffix: probes
extension: .tsv
inherit: true
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