Whole-slide microscopy image stitching and registration in Python
Ashlar performs fast, high-quality stitching of microscopy images. It also co-registers multiple rounds of cyclic imaging for methods such as CyCIF and CODEX. Ashlar can read image data directly from BioFormats-supported microscope vendor file formats as well as a directory of plain TIFF files. Output is saved as pyramidal, tiled OME-TIFF.
Note that Ashlar requires unstitched individual "tile" images as input, so it is not suitable for microscopes or slide scanners that only provide pre-stitched images.
Visit https://labsyspharm.github.io/ashlar/ for the most up-to-date information on ASHLAR.