napari-openuc2-processor

A self-contained napari plugin to download and process openUC2 / ImSwitch microscopy datasets.

pip install -e .
# open the downloader pre-filled with a source:
napari --plugin openuc2-processor 13457227.zarr
napari --plugin openuc2-processor "http://HOST:PORT/imswitch/api/FileManager/download/recordings/exp.ome.zarr"
napari --plugin openuc2-processor /path/to/local/tiles
# show a local OME-Zarr / OME-TIFF (pixel size, stage position, channels):
napari --plugin openuc2-processor /path/to/run/stitched.ome.tif

Features

• Dataset Downloader widget
  • Source can be a local path, a full http(s) URL, or a bare numeric ID (resolved against a configurable base — Zenodo by default).
  • Configurable storage directory (default ~/Downloads, "Change…" button).
  • Progress bar with Start / Stop / Restart.
  • Optional "load into napari as a stack/layer when done".
• OME viewing without napari-ome-zarr: a local OME-Zarr (image, plate or folder of images) or OME-TIFF opens with its pixel size, stage position, channel names and colours, display range and resolution pyramid, so the tiles of an ImSwitch run line up as a mosaic. The pixels are read lazily.
• Dataset Processor widget — a GUI over the ImSwitch tile-conversion engine (composite, stitch, mip, mip-composite, focus, tile-config, timelapse, timelapse-mip, ashlar). Pick an input folder, select modes, run, and optionally visualize the results in napari (otherwise they are just saved).

Extending

• New processing mode: add one Processor entry to openuc2_processor/processing/registry.py. The engine call and the widget checkbox appear automatically.
• New download source: add a Source subclass under openuc2_processor/sources/ and register it in resolve_source.

The processing engine is vendored from scripts/convert_experiment_tiffs.py in the ImSwitch repo and kept in sync manually; the standalone CLI script remains usable on its own.