Individual skill
nwb-conversion
Converts neuroscience acquisition data to Neurodata Without Borders files with NeuroConv and PyNWB, preserves metadata and timebases, checks evidence-based clock alignment, and produces schema validation, NWB Inspector findings and round-trip checks. Use for NWB conversion and synchronization of planar single-channel two-photon TIFF imaging plus timestamped behavioral position CSV; this skill does not perform spike sorting or claim tested support for arbitrary acquisition formats.
skills/nwb-conversion/SKILL.md
Source commit 2d2065fb4520fa3f3f2bcf61cff26ec8b7eba4b5
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- Last checked
- Nov 10, 2026
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- Repository last updated
- Nov 9, 2026
- License
- MIT
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- ai-scientist Repository topic
- bioinformatics Repository topic
- chemoinformatics Repository topic
- claude Repository topic
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SKILL.mdcore · 7,581 bytesSKILL.mdcore · 7,581 bytesSKILL.mdcore · 7,581 bytesSKILL.mdcore · 7,581 bytesSKILL.mdcore · 7,581 bytesSKILL.mdcore · 7,581 bytesSKILL.mdcore · 7,581 bytesassets/session-template.jsonasset · 1,340 bytesreferences/input-contract.mddoc · 4,842 bytesreferences/upstream-review.mddoc · 4,023 bytesscripts/convert_session.pyruns · 16,098 bytes
Read excerpt
# Validated NWB conversion
## Supported streams
The executable workflow covers two explicit input streams in one session:
| Input | NWB representation | Tested constraints |
| --- | --- | --- |
| Two-photon grayscale multi-page TIFF + frame timestamps CSV | Acquisition `TwoPhotonSeries` named `Imaging` through NeuroConv | One channel, one plane, one 2D image per page, fixed shape and dtype |
| Calibrated position CSV (`time_s,x,y`) | Behavior `Position` / `SpatialSeries` through PyNWB | Coordinates in m, cm or mm; converted to meters without temporal resampling |
Other acquisition readers require their own format-specific tests. In particular, this helper does
not decode SpikeGLX, Open Ephys, multichannel TIFF, volumetric TIFF, compressed video, or pixel-to-world
calibration. Do not rename an arbitrary numeric table to a supported stream.