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coverage example workflow PyPI version Ruff

NiLabels

NiLabels is a cacophony of tools to automate simple manipulations and measurements of medical image segmentations in nifti format. It is strongly based on and influenced by the library NiBabel

Introductory examples

1 Manipulate labels: relabel

Given a segmentation, imagine you want to change the labels values from [1, 2, 3, 4, 5, 6] to [2, 12, 4, 7, 5, 6] and save the result in my_new_segm.nii.gz. Then:

import nilabels as nil


nil_app = nil.App()
nil_app.manipulate_labels.relabel('my_segm.nii.gz', 'my_new_segm.nii.gz',  [1, 2, 3, 4, 5, 6], [2, 12, 4, 7, 5, 6])

2 Manipulate labels: clean a segmentation

Given a parcellation for which we expect a single connected component per label, we want to have it cleaned from all the extra components, merging them with the closest labels.

import nilabels as nil


nil_app = nil.App()

nil_app.check.number_connected_components_per_label('noisy_segm.nii.gz', where_to_save_the_log_file='before_cleaning.txt')
nil_app.manipulate_labels.clean_segmentation('noisy_segm.nii.gz', 'cleaned_segm.nii.gz', force_overwriting=True)
nil_app.check.number_connected_components_per_label('cleaned_segm.nii.gz', where_to_save_the_log_file='after_cleaning.txt')

Before cleaning check.number_connected_components_per_label would return:


Label 0 has 1 connected components
Label 1 has 13761 connected components
Label 2 has 14175 connected components
Label 3 has 14373 connected components
Label 4 has 1016 connected components
Label 5 has 806 connected components
Label 6 has 816 connected components
Label 7 has 1281 connected components
Label 8 has 977 connected components
Label 9 has 746 connected components

The same command after cleaning:

Label 0 has 1 connected components
Label 1 has 1 connected components
Label 2 has 1 connected components
Label 3 has 1 connected components
Label 4 has 1 connected components
Label 5 has 1 connected components
Label 6 has 1 connected components
Label 7 has 1 connected components
Label 8 has 1 connected components
Label 9 has 1 connected components

More tools are introduced in the documentation.

Instructions

Development

nilabel is a python package managed with poetry and linted with ruff, tested with pytest

TODO

Other than the many TODOs around the code, there are two more things:

  • typechecking with mypy
  • migrate from cicleCI to github workflows

Licencing and Copyright

Copyright (c) 2017, Sebastiano Ferraris. NiLabels (ex. LABelsToolkit) is provided as it is and it is available as free open-source software under MIT License

Acknowledgements

  • This repository had begun within the GIFT-surg research project.
  • This work was supported by Wellcome / Engineering and Physical Sciences Research Council (EPSRC) [WT101957; NS/A000027/1; 203145Z/16/Z]. Sebastiano Ferraris is supported by the EPSRC-funded UCL Centre for Doctoral Training in Medical Imaging (EP/L016478/1) and Doctoral Training Grant (EP/M506448/1).