MicroCorrelate#

A Python library for correlative microscopy workflows: stitch multi-tile acquisitions from Thermo Fisher Maps and register images across modalities.

Overview#

MicroCorrelate covers three areas:

  • Stitching: assemble tiled datasets from the Thermo Fisher Maps software into TIFF or OME-Zarr files, with pixel size and stage position preserved in the metadata.

  • Registration: align images from different modalities onto a common coordinate system via intensity-based registration (SimpleITK) or interactive landmark placement (Napari).

  • I/O: read common correlative microscopy formats including TIFF, HDF5 (LA-ICP-MS), OME-Zarr, and ToF-SIMS text files.

Installation#

pip install microcorrelate

See Examples for usage.