[BEP032]: add microelectrode electrophysiology example dataset by bendichter · Pull Request #527 · bids-standard/bids-examples

bendichter · 2025-12-29T14:28:27Z

This example dataset demonstrates the BIDS microelectrode electrophysiology
(microephys) specification for both extracellular (ecephys) and intracellular
(icephys) recordings.

Features Demonstrated

This dataset demonstrates the following key features:

Registration to Allen CCF v3 space: Electrode positions are provided in
Allen Common Coordinate Framework v3 (see space-AllenCCFv3 files)
Multiple probes in a single subject: sub-mouse01 uses two probes
simultaneously (probe01 and probe02) targeting different brain regions
Probe defined in ProbeInterface Library: probe01 uses the
A1x32-Poly3-10mm-50-177 model from the ProbeInterface library, referenced
via TermURL in the probes.json sidecar
Probe defined using a custom ProbeInterface definition: probe02 uses a
custom probe definition stored in the probes/ directory, referenced via
BIDS URI (bids::probes/customprobe1.json)

added by @yarikoption now that #515 is merged:

BIDS Specification PR: [ENH]: BEP032 formal review bids-specification#2307
BIDS Validator PR: NONE

Add microephys dataset demonstrating extracellular (ecephys) and intracellular (icephys) recordings in NWB format to the dataset listing.

ree-gupta · 2026-01-04T16:21:17Z

Hi Ben, thank you for contributing this! could you please rename the dataset directory to something more specific such that we can distinguish it from more future datasets? Perhaps, microephys_toy or anything else that is suitable?

Linking my PRs here to the @bids-standard/bep032 branch for completeness:

Updating existing icephys data on this branch: [BEP032] Add updated old icephys dataset #490 - it passes validation but a review from others would be nice
Updating/adding existing ecephys reach2grasp dataset: [BEP032] Add reach to grasp ecephys dataset #491

…Allen CCF coords - Move ecephys metadata files from session to subject level directory - Remove session identifier from channels, electrodes, and probes filenames - Add Allen CCFv3 coordinate system JSON with spatial reference metadata - Add electrode positions table with 32 electrodes mapped to Allen CCF space

bendichter · 2026-01-04T16:30:43Z

The good news is this almost works validating against the compiled BEP32 PR: bids-standard/bids-specification#1705. The bad news is it does not work 100% and I don't know why:

% bst -v export --schema src/schema --output src/schema.json

% bids-validator -s file:///Users/bdichter/dev/bids-specification/src/schema.json /Users/bdichter/dev/bids-examples/microephys/                  
        [ERROR] MICROEPHYS_SPACE_MISMATCH The space entity in electrodes.tsv must match the space entity in the
corresponding coordsystem.json file for microelectrode electrophysiology data.

                /sub-mouse01/ecephys/sub-mouse01_space-AllenCCFv3_electrodes.tsv

        Please visit https://neurostars.org/search?q=MICROEPHYS_SPACE_MISMATCH for existing conversations about this issue.

        [ERROR] MICROEPHYS_ELECTRODES_SPACE_REQUIRED If a coordsystem.json file with a space entity is present for microelectrode
electrophysiology data, a corresponding electrodes.tsv file with the same
space entity must also be present.

                /sub-mouse01/ecephys/sub-mouse01_space-AllenCCFv3_coordsystem.json

        Please visit https://neurostars.org/search?q=MICROEPHYS_ELECTRODES_SPACE_REQUIRED for existing conversations about this issue.

        [ERROR] EMPTY_FILE Empty files not allowed.
                /sub-mouse01/ses-01/ecephys/sub-mouse01_ses-01_task-rest_ecephys.nwb
                /sub-mouse01/ses-01/ecephys/sub-mouse01_ses-01_task-reach_ecephys.nwb

                1 more files with the same issue

        Please visit https://neurostars.org/search?q=EMPTY_FILE for existing conversations about this issue.


          Summary:                         Available Tasks:                 Available Modalities:
          24 Files, 15.6 kB                Reach to Grasp                   microephys           
          2 - Subjects 1 - Sessions        Resting State                                         
                                           IV Curve Characterization                             

        If you have any questions, please post on https://neurostars.org/tags/bids.

The empty files are not an issue-- this repo specifically requests them. The problem is the space validation. I'm pretty sure I added those correctly but they are not validating.

@yarikoptic and @ree-gupta , you both know the schema validation stuff better than I do. Any ideas?

- Add probes.json sidecar with NeuroNexus A1x32-Poly3-10mm-50-177 model description and reference URL - Add model column to probes.tsv - Update manufacturer from IMEC to NeuroNexus to match probe model

…-examples into bep32-microephys

- Rename microephys directory to microephys_toy for clarity - Add "Features Demonstrated" section highlighting key BIDS features: - Allen CCF v3 space registration - Multiple probes per subject - ProbeInterface library references - Custom probe definitions via BIDS URIs - Update dataset structure to document dual-probe setup (probe01/probe02) - Add customprobe1.json ProbeInterface definition for 16-channel probe

Add 16 new electrode entries (e033-e048) for probe02 targeting the right hemisphere CA1 hippocampal region with iridium contacts in the sub-mouse01 electrode coordinates file.

ree-gupta · 2026-01-04T17:33:40Z

The good news is this almost works validating against the compiled BEP32 PR: bids-standard/bids-specification#1705. The bad news is it does not work 100% and I don't know why:

Hi @bendichter , thanks again. It was to do with the associations files. The original validation failed because the coordsystem association lacked entities: - space in its target. Without this, the association lookup ignored the space entity when finding coordsystem files - so an electrodes.tsv with space-AllenCCFv3 could match ANY coordsystem.json regardless of its space entity, causing false MICROEPHYS_SPACE_MISMATCH
errors.

Adding entities: - space ensures the association only finds coordsystem files with matching space values. The check associations.coordsystem != null now implicitly verifies both existence AND space matching.

I also improved the comments in the schema files.

I cloned your fork, and checked, it passes the validation now 🎉

bendichter · 2026-01-04T17:38:24Z

yay! I can confirm the fix worked 💯

bendichter · 2026-01-04T17:38:50Z

From my perspective this is ready

ree-gupta · 2026-01-04T17:55:43Z

From my perspective this is ready

I get a couple of errors:

TSV_COLUMN_ORDER_INCORRECT Some TSV columns are in the incorrect order: we did not explicitly discuss this. Some modalities use a specific order and I had done the same but without very strong rationale. We could either simply align with iEEG or leave it out, that is, not specify any order.
PharmaceuticalName/PharmaceuticalDoseUnits should be strings (not arrays) : should we discuss?
SampleEnvironment needs valid enum ("in vivo" not "in-vivo")
issue with the custom probe - I am looking into this, will fix this one

bendichter · 2026-01-04T18:05:29Z

Huh I didn't see these in the valuation errors

ree-gupta · 2026-01-04T18:15:35Z

Huh I didn't see these in the valuation errors

Surprisingly the probes error went away when I used, deno cache --reload jsr:@bids/validator with no changes to the schema at all. Could you please run the validator one more time and report what you see?

bendichter · 2026-01-04T19:09:07Z

ok I recompiled and now I am getting the errors you mentioned. I will let you know when they are all fixed.

Move x, y, z columns adjacent to each other and relocate hemisphere column after z coordinate for better logical grouping in electrodes TSV.

…ufacturer Move the 'model' column from position 3 to after 'manufacturer' column, improving logical grouping of device-related metadata fields.

…dinates Move the hemisphere column from position 3 to position 6 in sub-mouse02_electrodes.tsv, placing it after the x, y, z coordinate columns for improved logical grouping of spatial information.

Move x, y, z columns together after probe_name and relocate hemisphere column after z coordinate for more logical data organization.

…ive atlas IDs - Add CogAtlasID references for task definitions - Convert PharmaceuticalName and PharmaceuticalDoseUnits from arrays to strings - Fix SampleEnvironment format: "in-vivo"/"ex-vivo" → "in vivo"/"ex vivo" - Add missing RecordingDuration field to IVcurve task metadata

bendichter · 2026-01-04T19:29:51Z

@ree-gupta ok, fixed!

dataset_listing.tsv

ree-gupta · 2026-01-06T08:16:38Z

We need to remove dimension_unit use (ref bids-standard/bids-specification@ad50350), otherwise looks good to me!

yarikoptic · 2026-01-16T03:30:06Z

Note that I have added testing against our BEP032 PR schema changes. Unfortunately testing fails

	Please visit https://neurostars.org/search?q=SIDECAR_KEY_RECOMMENDED for existing conversations about this issue.

	[ERROR] TSV_COLUMN_MISSING A required column is missing
		electrode_name
		/sub-mouse01/ecephys/sub-mouse01_channels.tsv - Required initial column 2 not found.
		/sub-mouse02/icephys/sub-mouse02_channels.tsv - Required initial column 2 not found.

	Please visit https://neurostars.org/search?q=TSV_COLUMN_MISSING for existing conversations about this issue.

	[ERROR] TSV_ADDITIONAL_COLUMNS_MUST_DEFINE Additional TSV columns must be defined in the associated JSON sidecar for this file type
		dimension_unit
		/sub-mouse01/ecephys/sub-mouse01_probes.tsv

	Please visit https://neurostars.org/search?q=TSV_ADDITIONAL_COLUMNS_MUST_DEFINE for existing conversations about this issue.


          Summary:                         Available Tasks:                 Available Modalities:
          26 Files, 21.9 kB                Reach to Grasp                   microephys           
          2 - Subjects 1 - Sessions        Resting State                                         
                                           IV Curve Characterization

ree-gupta · 2026-01-16T07:29:27Z

Also take a look here: #491 - it is reviewed and complete and passes the validator.

- Add required electrode_name column to channels.tsv (ecephys and icephys) - Remove deprecated dimension_unit column from probes.tsv - Convert probe width/height/depth values from um to mm - Remove optional reference column from channels.tsv Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

CodyCBakerPhD · 2026-03-18T15:12:48Z

@bendichter @ree-gupta what would you like to do with this one? Looks like there are conflicts to resolve in order to retrigger dev tests against the BEP branch

feat: add microelectrode electrophysiology example dataset

f249e51

Add microephys dataset demonstrating extracellular (ecephys) and intracellular (icephys) recordings in NWB format to the dataset listing.

bendichter mentioned this pull request Dec 29, 2025

[ENH] microelectrode electrophysiology specification (BEP032) bids-standard/bids-specification#1705

Closed

22 tasks

bendichter changed the title ~~feat: add microelectrode electrophysiology example dataset~~ feat: add microelectrode electrophysiology example dataset (BEP032) Jan 4, 2026

bendichter changed the title ~~feat: add microelectrode electrophysiology example dataset (BEP032)~~ [BEP032]: add microelectrode electrophysiology example dataset Jan 4, 2026

bendichter added 5 commits January 4, 2026 11:34

Merge branch 'master' into bep32-microephys

9965a6e

feat(ecephys): add probe model metadata for sub-mouse01

d74071d

- Add probes.json sidecar with NeuroNexus A1x32-Poly3-10mm-50-177 model description and reference URL - Add model column to probes.tsv - Update manufacturer from IMEC to NeuroNexus to match probe model

Merge branch 'bep32-microephys' of https://github.com/bendichter/bids…

7cbce15

…-examples into bep32-microephys

feat(data): add probe02 electrode entries for CA1 region

5067802

Add 16 new electrode entries (e033-e048) for probe02 targeting the right hemisphere CA1 hippocampal region with iridium contacts in the sub-mouse01 electrode coordinates file.

bendichter added 5 commits January 4, 2026 14:27

refactor: reorder electrode columns to group spatial coordinates

b69a726

Move x, y, z columns adjacent to each other and relocate hemisphere column after z coordinate for better logical grouping in electrodes TSV.

refactor(ecephys): reorder probes.tsv columns to group model with man…

4af59b6

…ufacturer Move the 'model' column from position 3 to after 'manufacturer' column, improving logical grouping of device-related metadata fields.

fix: reorder columns in electrodes TSV to place hemisphere after coor…

a3cc090

…dinates Move the hemisphere column from position 3 to position 6 in sub-mouse02_electrodes.tsv, placing it after the x, y, z coordinate columns for improved logical grouping of spatial information.

refactor: reorder electrode TSV columns to group spatial coordinates

b28a843

Move x, y, z columns together after probe_name and relocate hemisphere column after z coordinate for more logical data organization.

bendichter commented Jan 4, 2026

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This was referenced Jan 15, 2026

[ENH]: BEP032 formal review bids-standard/bids-specification#2307

Open

[BEP032] Add reach to grasp ecephys dataset #491

Open

This was referenced Jan 15, 2026

[BEP032] Add updated old icephys dataset #490

Closed

Draft examples for BEP032 on animal electrophysiology #430

Draft

Merge branch 'master' into bep32-microephys

0d03a4d

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