Minisim
From Miniscope
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Minisim builds a miniscope recording *forward* from its physical components, the inverse of an analysis pipeline like [minian](https://github.com/miniscope/minian). Instead of recovering signals from a movie, it starts from biology and optics and produces the movie, together with the ground truth that generated it:
place neurons -> cell activity -> bleaching -> optics -> composite -> neuropil -> brain motion -> illumination profile -> vignette -> leakage -> image sensor
Each stage is a small, inspectable physical model. Because the recording is built forward, every recording ships with exact ground truth (cell locations,
footprints, calcium traces, spike times, motion trajectory, per-pixel optical fields), which makes Minisim useful for:
- Benchmarking calcium-imaging pipelines (minian, CaImAn, suite2p, ...) against known ground truth.
- Teaching the anatomy of miniscope data: what each physical effect does to the image, via interactive notebooks.
- Testing analysis code with reproducible, parameterized fixtures.
Full documentation: minisim.readthedocs.io: concepts, quickstart, how-to guides, and the API reference.