A simple Python library for handling correlative microscopy datasets
Project description
MicroCorrelate
A simple Python library for handling correlative microscopy datasets.
Visit the MicroCorrelate website for the full documentation.
Features
- Stitching: assemble tiled datasets from Thermo Fisher Maps into single TIFF or OME-Zarr files, with physical pixel size and stage position metadata
- Intensity-based registration: automatic multi-modal image registration via SimpleITK (affine, rigid, similarity transforms)
- Landmark-based registration: interactive registration using a Napari viewer for manual point placement
Installation
We recommend installing the package in a fresh environment:
pip install microcorrelate
Command-line interface
A stitch-maps command is available after installation for stitching tiled
datasets from Thermo Fisher Maps:
stitch-maps --source data/LayersData/tileset --dest out/stitched.zarr --verbose
Run stitch-maps --help for the full list of options.
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