plate-overview

Whole-plate overview images for multiwell fluorescence microscopy: one thumbnail per well, laid out in plate geometry, with each channel's contrast normalized across the whole plate so wells are comparable to each other by eye.

Vendor-neutral. This package knows nothing about acquisition formats — you hand it pixels through a small typed port and it draws.

Status: pre-alpha, empty. The renderer has not landed yet. See ferrinm/PyPhenix#32, which extracts it, and #1 here.

Why this exists as its own package

There is exactly one renderer. Every acquisition format reaches it through an adapter, so overviews from different instruments stay comparable. pyphenix (Opera Phenix) is the first consumer. A Leica Thunder .lif adapter is the second.

Design notes

CONTEXT.md covers the render port, the gathering loop, and the resampling rule.

Install

pip install plate-overview

Contributing

Two house rules beyond the usual:

• No real acquisition data, anywhere. No fixture, example, sidecar or docstring may derive from a real acquisition. No plate identifiers, no operator-bearing paths, no source filenames. Test fixtures are synthetic. This repository is public and the upstream acquisitions are not.
• Output paths are basenames. The JSON sidecar records a filename, never an absolute path, so a sidecar pasted into an issue does not leak a filesystem layout.

License

BSD 3-Clause. See LICENSE.