Lab Scripts

A central toolbox of the small, single-purpose scripts written for people in the lab over the years. One repo so they stay findable, versioned, and reproducible — no more chasing copies across shared drives and USB sticks.

Looking to learn rather than run something? Tutorials, guides, and curated resources live in Lab-Libraries. This repo holds the runnable tools; that one holds the knowledge.

How it's organized

• Scripts are grouped by domain (not by person — people leave, domains stay).
• Each script lives in its own folder with a short README.md: what it does and an example command. No names or dates — those are personal info, keep them out.
• Dependencies are declared per script so an old script still runs years later.

lab-scripts/
├── README.md                      # this index
├── CONTRIBUTING.md                # how to add a new script
├── _template/                     # copy this to start a new script
├── image-conversion/
│   └── tiff-to-avi/               # compile TIFF sequences into AVI/MP4 (GPU-accelerated)
├── data-conversion/
│   └── csv-to-hdf5/               # convert CSV files into HDF5 (.h5)
├── mesh-generation/
│   └── cells-to-stl/              # turn cell coordinates (CSV/Excel) into a 3D STL mesh
└── neuro-visualization/
    └── brainrender/               # render 3D brain scenes (regions, meshes, probes) via BrainRender

Script index

Domain	Script	What it does
image-conversion	tiff-to-avi	Compile thousands of TIFFs into an AVI/MP4 video, GPU-accelerated
data-conversion	csv-to-hdf5	Convert one or many CSV files into HDF5 (.h5) files
mesh-generation	cells-to-stl	Turn cell coordinates (CSV/Excel) into a 3D STL mesh of spheres
neuro-visualization	brainrender	Render 3D brain scenes (regions, meshes, probes, rulers) via BrainRender

Add a row here whenever you add a script.

Running a script

Scripts declare their own dependencies inline (PEP 723), so the simplest reproducible way to run one is with uv:

uv run image-conversion/tiff-to-avi/convert_tiff_to_avi.py

uv reads the dependency block at the top of the file, builds an isolated environment, and runs it — no manual venv, no pip install. Some scripts also need external binaries (e.g. ffmpeg); those are noted in each script's README.

Adding a script

See CONTRIBUTING.md. In short: copy _template/, drop your script in, fill in its README, declare its deps inline, and add a row to the index above.