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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