atlas_tools

Tools for analysis of large image datasets created with Light-Sheet Fluorescence Microscopy (LSFM). Includes atlas registration, data structure organization, simple image processing (detection of vessels, alveoli, simple cells). Copyright 2024 Ludovico Silvestri. Use granted for research and not-for-profit purposes. All other uses are prohibited.

Name		Name	Last commit message	Last commit date
Latest commit History 163 Commits
.gitignore		.gitignore
Dockerfile		Dockerfile
README.md		README.md
alveoli_detector.py		alveoli_detector.py
atlas_affine_generator.py		atlas_affine_generator.py
atlas_initial_transform_generator.py		atlas_initial_transform_generator.py
blob_eval.py		blob_eval.py
blob_utils.py		blob_utils.py
composite.py		composite.py
conncomp.py		conncomp.py
dog_filter.py		dog_filter.py
downscale.py		downscale.py
filterimage.py		filterimage.py
makeRGB.py		makeRGB.py
maskmaker.py		maskmaker.py
merge2sides.py		merge2sides.py
merge2sides16.py		merge2sides16.py
mergePC.py		mergePC.py
midres_gen.py		midres_gen.py
midres_single.py		midres_single.py
nifti2tif.py		nifti2tif.py
niftiutils.py		niftiutils.py
npy2marker.py		npy2marker.py
organize_folder.py		organize_folder.py
prepare1side.py		prepare1side.py
prepare2sides.py		prepare2sides.py
prepare2sides16.py		prepare2sides16.py
preparePC.py		preparePC.py
preparePC_old.py		preparePC_old.py
random_substack_generator.py		random_substack_generator.py
requirements.txt		requirements.txt
tif2nifti.py		tif2nifti.py
vesselness_filter.py		vesselness_filter.py
vessels.py		vessels.py
zip2substack.py		zip2substack.py

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