PixelPatrol add-on package for loading images with bioio and zarr
Project description
PixelPatrol Bio-Image Loader Extension (pixel-patrol-loader-bio)
This extension provides three loaders for multi-dimensional life-science imaging formats.
Loaders
bioio — BioIO (CZI, LIF, ND2, TIFF, rasters)
Uses the BioIO library for broad format support.
.czi— Zeiss CZI.lif— Leica LIF.nd2— Nikon ND2.tif,.tiff,.ome.tif— TIFF via BioIO.jpg,.jpeg,.png,.bmp— common raster formats.zarr,.ome.zarr— zarr stores via BioIO
tifffile — TiffFile (TIFF / OME-TIFF)
Direct TIFF loading via tifffile with lazy Zarr-backed access.
.tif,.tiff,.ome.tif— including multi-series OME-TIFF- Lighter than
bioiofor TIFF-only datasets
zarr — Zarr (zarr / OME-Zarr)
Native zarr store loading with OME-NGFF axis support.
.zarr,.ome.zarr
Installation
uv pip install pixel-patrol-loader-bio
Or as part of the full stack:
uv pip install pixel-patrol
Getting Started
Please see the pixel-patrol documentation for usage instructions.
https://github.com/ida-mdc/pixel-patrol/
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