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CodyCBakerPhD merged 3 commits into from
Jan 23, 2026
Merged

Add conversion gallery documentation for NWB to BIDS mapping #286

CodyCBakerPhD merged 3 commits into from
Jan 23, 2026

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Copilot AI commented Jan 23, 2026 •
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Adds documentation section demonstrating fine-grained NWB file content extraction to BIDS sidecars per BEP32. Located after tutorials, uses same ecephys example data.

Changes

  • docs/conversion_gallery.rst - New 450+ line documentation covering:

    • Reading NWB files with PyNWB (devices, electrode tables, ElectricalSeries)
    • BIDS sidecar generation (probes.tsv, electrodes.tsv, channels.tsv)
    • Field-to-field mapping tables for each metadata type
    • Subject/session metadata extraction to participants.tsv, sessions.tsv

  • docs/index.rst - Added conversion_gallery to toctree after tutorials

  • docs/conftest.py - Extended setup to pre-convert tutorial data for gallery examples

Example

Shows how NWB electrode table maps to BIDS sidecars:

# Read from NWB
electrodes_table = nwbfile.electrodes.to_dataframe()
# location, group_name, imp, filtering columns

# Extract to BIDS
bids_electrodes_df = pd.read_csv("sub-001_ses-A_electrodes.tsv", sep="\t")
# name, probe_name, location, impedance columns

Includes complete mapping tables like:

NWB Field BIDS Field
electrodes.id name
electrodes.group.device.name probe_name
electrodes.imp impedance (kOhms)

Screenshot

Conversion Gallery

All code examples are executable and doc-tested (32 tests).

Original prompt

This section details on the original issue you should resolve

<issue_title>Add conversion gallery</issue_title>
<issue_description>Showcasing the fine-grain file contents in line with BEP32</issue_description>

<agent_instructions>This should be a section of the docs after the tutorial that uses the same data but goes deep into the content of each NWB file (using PyNWB to read and display) and shows side-by-side what is extracted into BIDS sidecars</agent_instructions>

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Copilot AI changed the title [WIP] Add conversion gallery to showcase file contents Add conversion gallery documentation for NWB to BIDS mapping Jan 23, 2026
Copilot AI requested a review from CodyCBakerPhD January 23, 2026 03:04
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codecov bot commented Jan 23, 2026 •
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Codecov Report

✅ All modified and coverable lines are covered by tests.
⚠️ Please upload report for BASE (conversion_gallery@84ce669). Learn more about missing BASE report.

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  Partials                      ?        0
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@CodyCBakerPhD
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CodyCBakerPhD commented Jan 23, 2026

@copilot Could you fix the pre-commit? Do you know why you didn't do it in the first place (given it is specified in the copilot instructions)

@CodyCBakerPhD CodyCBakerPhD changed the base branch from main to conversion_gallery January 23, 2026 03:31
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CodyCBakerPhD commented Jan 23, 2026

@copilot Nevermind, I'll deal with it myself. This is a good start, thank you

@CodyCBakerPhD CodyCBakerPhD marked this pull request as ready for review January 23, 2026 03:31
@CodyCBakerPhD CodyCBakerPhD merged commit 17a4b7f into conversion_gallery Jan 23, 2026
54 of 56 checks passed
@CodyCBakerPhD CodyCBakerPhD deleted the copilot/add-conversion-gallery branch January 23, 2026 03:31
Copilot stopped work on behalf of CodyCBakerPhD due to an error January 23, 2026 03:32
The session was cancelled by the user.
CodyCBakerPhD added a commit that referenced this pull request Jan 28, 2026
@CodyCBakerPhD
@pre-commit-ci @asmacdo
Added conversion gallery showcasing NWB to BIDS field mappings (#288)
f0fb725 
* Add conversion gallery documentation for NWB to BIDS mapping (#286)

* Initial plan

* Add conversion gallery documentation with NWB to BIDS mapping examples

Co-authored-by: CodyCBakerPhD <[email protected]>

* Fix conversion gallery assertions and improve metadata descriptions

Co-authored-by: CodyCBakerPhD <[email protected]>

---------

Co-authored-by: copilot-swe-agent[bot] <[email protected]>
Co-authored-by: CodyCBakerPhD <[email protected]>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* wip

* polishing probes

* polishing probes

* finish draft

* finish draft

* Update docs/conversion_gallery.rst

Co-authored-by: Austin Macdonald <[email protected]>

* Apply suggestions from code review

* Update docs/conftest.py

Co-authored-by: Austin Macdonald <[email protected]>

* Delete docs/expected_files/sub-001_ses-A_ecephys.nwb

* fix alignment

* Update docs/conversion_gallery.rst

Co-authored-by: Austin Macdonald <[email protected]>

---------

Co-authored-by: Copilot <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Austin Macdonald <[email protected]>
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