Community Review: BEP032 - Microelectrode Electrophysiology

[effigies]

We are pleased to announce the community review period for BIDS Extension Proposal (BEP) 032!

BEP032 extends the BIDS standard to describe microelectrode electrophysiology data.

The draft specification may be found at: https://bids-specification--2307.org.readthedocs.build/en/2307/, with the most significant changes in Modality specific files - Microelectrode Electrophysiology.

The proposed changes may be found at #2307. To view the source difference, click the Files changed tab.

Example datasets may be found at:

• microephys_ecephys_multielectrode_grasp
• microephys_toy

Procedure

Review period

Community review is open from April 20 - May 1, 2026.

Voting

This discussion is a poll, which you can vote in once and cannot change your response. Therefore, please vote once you are satisfied that your answer will not change.

If you vote "No", you may create a thread to explain your reasoning or send a private email to bids.maintenance [at] gmail.com so that your position can be fully understood.

How to review

Use threads in this discussion to request clarification or changes to the BEP. Each independent topic or proposed change should have its own thread. Please review existing threads and consider adding comments to those, if your topics are already being discussed. If your concerns are adequately represented by an existing comment or comments, consider using the 👍🏻 reaction button to indicate agreement in place of extending the discussion.

Where possible, propose the specific text you would like to see added or removed.

For minor issues, such as typos, feel free to make code suggestions only, using the suggest feature on the BEP032 pull request. These suggestions may be accepted or rejected without discussion, so do not make substantial proposals in this way.

Finalization

Once the review period is finished, the BEP leads and maintainers will consider the entire discussion, identify outstanding points to be resolved, and work toward finalizing the BEP. Community members may be asked to participate in this process to provide the necessary expertise.

Before being merged, the BEP will be integrated into the BIDS validator, and the example (1 and 2) must pass the validator.

A BIDS 1.12.0 release is anticipated in late spring/early summer 2026, regardless of the conclusion of this specific BEP.

If, for any reason, a critical issue is found after the BEP is merged, the BEP will be reverted while the issues are addressed. At the discretion of the BIDS steering group and maintainers group, depending on the scope of changes, a new community review period may be opened.

[saskiad]

I think this is missing too much crucial information for understanding these data.

[CodyCBakerPhD]

@saskiad Thanks for taking a look - could you elaborate on which aspects you would like to see improved?

[saskiad]

A few things:
I don't see where I provide important information about the subject - I know some of it lives outside the ephys part, but I don't see where I would provide (e.g.) genotype or virus information or where the virus is injected. If I'm optotagging units or if I'm doing patch recordings of specifically identified neurons, that information becomes important.
The task information maybe works for human cognitive tasks, but not for most animal behavior or stimuli.
The processing information seems to just be about filtering, which is not the only processing.
Slice thickness, but no information about where the slice is or what orientation
For ecephys we often target many different brain structures simultaneously, how is that conveyed? (I think there was something in the original note I saw about coordinates that I'm not finding anymore)
I think I'm missing where internal and external solutions live for icephys?

[CodyCBakerPhD]

@saskiad Thanks for getting back

One of the greatest things about BIDS is how flexible the TSV tables are in terms of attaching any additional metadata you may wish to include!

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I don't see where I provide important information about the subject - I know some of it lives outside the ephys part, but I don't see where I would provide (e.g.) genotype or virus information or where the virus is injected.

That would be a participant-level tabular column, such as those seen on this example: https://github.com/bendichter/bids-examples/blob/bep32-microephys/microephys_toy/participants.tsv

I want to say that the nwb2bids tool ought to already be extracting and including such information if and when available in the NWB files - did you have a dataset you would like me to check on to see what the BIDS extraction would look like?

The task information maybe works for human cognitive tasks, but not for most animal behavior or stimuli.

The task information is likewise extremely flexible; in our non-toy (real experiment) example dataset the events structure is essentially what you would find in the NWB contents, but extracted for convenience: https://github.com/ree-gupta/bids-examples/blob/bep032_ecephys_r2g/microephys_ecephys_multielectrode_grasp/sub-i/ses-140703/ecephys/sub-i_ses-140703_task-r2g_run-001_events.tsv

The processing information seems to just be about filtering, which is not the only processing.

A good amount of that is indeed kept as 'schematic intercompatability' inhereted from BIDS-iEEG, but there are also a fair number of people these days (even using Neuropixels) that are largely concerned with oscillations/ripples/lfp and so filtering is a very important detail to them

I will refer to lead author @ree-gupta if I forgot anything specific about filtering/processing justifications (which may be explained more thoroughly in the companion manuscript - does that have a biorxiv link yet?)

Slice thickness, but no information about where the slice is or what orientation

Ahh, we spent a fair amount of time thinking about icephys 'spaces' (both in vivo and ex vivo slices) - we had hoped that the existing coordsystem + space- JSON specifications would allow enough specificity about that, but if you could provide more specific counter examples or questions on that we'd happy to try and improve it!

Pinging @apdavison as they were our local 'icephys' expert on this effort

I recall @lzehl also had similar questions but we somehow explained/resolved them at the time or decided it was out of scope for this particular 'first step' towards a brighter future. Perhaps @lzehl recalls more than I

For ecephys we often target many different brain structures simultaneously, how is that conveyed? (I think there was something in the original note I saw about coordinates that I'm not finding anymore)

The great thing is this new metadata setup allows greater specificity on this aspect than NWB has ever allowed (well, besides maybe the new ndx-anatomical-localization)!

You can specify the probe-level insertion area and coordinates: https://github.com/ree-gupta/bids-examples/blob/bep032_ecephys_r2g/microephys_ecephys_multielectrode_grasp/sub-i/ses-140703/ecephys/sub-i_ses-140703_probes.tsv

The locations per electrode (physical contact): https://github.com/ree-gupta/bids-examples/blob/bep032_ecephys_r2g/microephys_ecephys_multielectrode_grasp/sub-i/ses-140703/ecephys/sub-i_ses-140703_electrodes.tsv

And you can use the channel mapping to do a 'look up' against those electrode linkages for fancy things like a NeuroPixels v2.0 setup (or you could also add an additional custom column for easy lookup in that case): https://github.com/ree-gupta/bids-examples/blob/bep032_ecephys_r2g/microephys_ecephys_multielectrode_grasp/sub-i/ses-140703/ecephys/sub-i_ses-140703_channels.tsv

I think I'm missing where internal and external solutions live for icephys?

Unsure - @apdavison @lzehl @ree-gupta? If not established, we can probably add something for that without too much difficulty

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I hope that answers all of your questions!

[bendichter]

Thanks for the thorough response, @CodyCBakerPhD.

I think a lot of what's coming up here is that the BEP is leaning heavily on existing BIDS infrastructure to carry subject- and anatomy-level metadata: participants.tsv, sessions.tsv, the coordsystem/space- JSONs, the sample-level fields. This is not very visible from the microephys page itself. It took us a few years of back-and-forth to work out how the needs of microephys map onto that existing structure, and prune the BEP down to just the essential additions. But a lot of that work is obscured here.

@saskiad, would you be open to meeting to walk through the specifics? I doubt we'd get a complete round-trip with AIND's metadata structure, but I think it would be useful to see concretely how much is captured by the proposed addition plus the surrounding BIDS scaffolding, and where the gaps are.

One scope point worth flagging: BIDS draws a hard line between raw and processed data, and this BEP is specifically for raw data, i.e., what comes off the acquisition system with minimal offline processing. Things like spike sorting results are very important, but we're intentionally saving those for a separate BEP. That may explain why the processing fields here look filter-centric.

[bendichter]

Following up here for the record: I discussed this with Saskia by email and she is fine with the proposal moving forward. Since her comments, the working group has moved anatomical location to the electrode level (#2481), added anatomical location and an extended sample_type vocabulary to samples.tsv (#2484), and made the sample entity required for icephys (#2480). Chris has confirmed that this resolves the thread.

[asmacdo]

I noticed that BodyPart is a free-form string with no list of acceptable values, whereas other modalities with this field are more prescriptive.

eg Microscopy https://bids-specification.readthedocs.io/en/stable/modality-specific-files/microscopy.html#sample

Body part of the organ / body region scanned. From DICOM Body Part Examined (for example "BRAIN").

[yarikoptic]

overall, I think we should submit (separately) clarification that for BodyPart itself SNOMED CT should be used, and even DICOM switched to it AFAIK and lists on that https://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html#chapter_L we reference now.

Overall, this one is not that informative for BIDS since it is concerned with BRAIN -- it is in its name, and so far proposal on adding cardio was not even accepted (might have changed). So, we could add clarification to point to SNOMED CT but BRAIN I would say "assumed" and we have further details to be provided with BodyPartDetails and BodyPartDetailsOntology per already existing fields like see https://bids-specification.readthedocs.io/en/stable/modality-specific-files/magnetic-resonance-imaging-data.html#tissue-description and then similar in this PR: https://bids-specification--2307.org.readthedocs.build/en/2307/modality-specific-files/microelectrode-electrophysiology.html#sample

[effigies]

The review period is officially over. There are outstanding discussions that need to be resolved before the BEP can be finally accepted and merged. You should be able to continue existing threads.

[bendichter]

We have reached out to @saskiad to discuss her feedback in more detail.