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@FabrizioMusacchio FabrizioMusacchio released this 30 Aug 21:41
· 52 commits to main since this release
v0.0.0
f0c6cf9

🚀 IntelliCage Place Learning Toolkit v0.0.0

August 30, 2026

This is the first public release of the IntelliCage Place Learning Toolkit, a Python toolkit for analyzing place learning experiments conducted in the IntelliCage. The release establishes the public package structure, synthetic example dataset, documentation entry points, and automated tests for the core loader, metric, and plotting workflow.

✨ Features

  • Added the public ic_placelearning Python package with loader, metric, and plotting modules.
  • Added IntelliCage export loading for cohort folders containing Mice.txt, Visits.txt, and Nosepokes.txt files across protocol phases.
  • Added metadata harmonization for mouse group, sex, RFID, experiment label, date of birth, and assigned phase-3/phase-4 corners.
  • Added aligned analysis-time columns for protocol-level phase windows, experiment elapsed time, phase elapsed time, mouse days, and awake/sleep summaries.
  • Added place-learning metrics for correct-corner visits, correct-corner nose-poke visits, rewarded correct-corner visits, and MATLAB-compatible PlaceError == 0 scoring.
  • Added phase-4 reversal metrics separating visits to the new correct corner, previous correct corner, and neutral incorrect corners.
  • Added binned activity, learning-rate, learning-count, responder, onset, phase-activity, cumulative-corner-role, and group-comparison summary functions.
  • Added plotting helpers for experiment overviews, phase-wise learning curves, reversal components, day-wise violins, onset distributions, cumulative role curves, and phase-activity summaries.

🗂 Example Data

  • Added a synthetic Group A/B IntelliCage-style dataset with 20 pseudo-mice and four protocol phases.
  • Added a reproducible synthetic data generator in additional_scripts/.
  • Added a public synthetic-data analysis script in user_scripts/.
  • Added generated protocol schematic assets in figures/ for README and documentation use.

📚 Documentation

  • Added public README documentation focused on installation, package structure, synthetic example data, demo analysis, metric definitions, time alignment, testing, and citation.
  • Added an IntelliCage place-learning protocol schematic for the four-phase workflow: Free Hab, NPA, PL, and PR.
  • Added CITATION.cff metadata for citation-aware repositories.
  • Added contribution guidelines tailored to IntelliCage place-learning analysis and synthetic-data-based testing.

🧪 Tests and packaging

  • Added pyproject.toml for editable installs and future PyPI packaging under the distribution name ic-placelearning.
  • Added development dependencies for testing and documentation via pip install -e ".[dev]".
  • Added automated tests for loader behavior, aligned timing, core metrics, statistical summaries, plotting smoke tests, synthetic data generation, and the public demo script.
  • Established a test coverage threshold of 75% for the public ic_placelearning package.
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