Lesion Segmentation Python Packages

bidsgate

Recovery gate for neuroimaging pipelines: inject known lesions or atrophy into real BIDS data, run any BIDS app, score what it recovered

tiramisu-brulee

A 2D and 3D PyTorch implementation of the Tiramisu CNN

samseg

Sequence Adaptive Multimodal SEGmentation (SAMSEG)

lesion-metrics

metrics for evaluating lesion segmentations

yolo-mslesseg

End-to-end pipeline for the automatic segmentation and evaluation of multiple sclerosis lesions in MRI images, built upon YOLOv11n-seg.

mindglide

Brain MRI segmentation for multiple sclerosis — any sequence, any quality. pip install mindglide