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NWB Neuroscience Conversion

Converts two-photon TIFF imaging and position CSV into validated NWB files with checked timing.

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
5 files

What it does

Once installed, the agent can convert a neuroscience recording (planar single-channel two-photon TIFF image stack plus frame timestamps, and a timestamped position CSV) into an NWB file, the standard archive format for neuroscience data. It keeps original metadata and timing, only aligns clocks when the user supplies matching evidence such as sync pulses, and runs schema validation, NWB Inspector checks and round-trip comparisons. It does not do spike sorting or support other acquisition formats.

Great for

  • Neuroscience labs converting single-plane two-photon imaging with behavioral position tracking into NWB
  • Data engineers who need reproducible, checksummed NWB conversions with a validation report
  • Students learning how NWB files are validated and how clock synchronization is checked

Skip it if

  • Recordings in SpikeGLX, Open Ephys, multichannel, volumetric or compressed video formats, since the skill states these are not tested or decoded and would need their own tests
  • Sessions without real clock evidence (shared clock or matched pulses), because the skill refuses to guess synchronization and wrong alignment would corrupt timing
  • Anyone expecting a file that is scientifically correct merely because validation passes; the skill itself warns that anatomical labels, pulse pairing and calibration still need human review

Try asking

  • “Convert my two-photon TIFF stack and frame_times.csv into an NWB file using this session.json config”
  • “Check this NWB file with NWB Inspector and explain any critical findings”
  • “Align position.csv to the imaging clock using the three sync pulses I recorded”
Step-by-step guide: how to use NWB Neuroscience ConversionInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 5 original files, the MIT licence and an attribution note.

    nwb-conversion.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip nwb-conversion.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip nwb-conversion.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Prepare a session JSON with real metadata (subject, timezone, units, clock source) rather than relying on the sample template defaults, which are synthetic.
  • Read the .validation.json report and the CLI summary, not just the exit code; exit zero does not mean the file is scientifically correct.
  • Use a fresh output path after any failed run, since a failed write can leave an incomplete NWB file without a report.

What's inside

  • assets/session-template.json
  • references/input-contract.md
  • references/upstream-review.md
  • scripts/convert_session.py
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.