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BrainLesion

10 indexed repositories · View on GitHub

BraTS
Providing top-performing algorithms from the Brain Tumor Segmentation (BraTS) challenges.

Python · 85 stars
preprocessing
preprocessing tools for multi-modal 3D brain imaging

C · 39 stars
panoptica
panoptica -- instance-wise evaluation of 3D semantic and instance segmentation maps

Python · 34 stars
tutorials
BrainLes tutotrials

Jupyter Notebook · 11 stars
AURORA
Segmentation models for cancer metastasis in brain MR

Python · 11 stars
GlioMODA
multi-modal MRI BraTS glioma segmentation for various sequence combinations

Python · 9 stars
PeTu
pediatric brain tumor segmentation models

Python · 6 stars
modsort
manual sorting GUI for identifying multi-modal MR sequences

Vue · 5 stars
stroke_segmentor
stroke segmentation in MRI data

Python · 4 stars
auxiliary
helpful functions for handling biomedical-imaging data in DICOM or NIfTI format

Python · 2 stars

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56 open issues indexed

[BUG] Modsort x86 Linux only runs from terminal with --no-sandbox add-on, does not open with double click Open

bug

BrainLesion/modsort#12 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[FEATURE] stroke segmentation needs to be integrated into the BrainLes paper Open

enhancement

BrainLesion/stroke_segmentor#3 · 4 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
[QUESTION] Preprocessing pediatric brain data Open

question

BrainLesion/PeTu#21 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
[BUG] Zenodo.py needs to be updated Open

bug

BrainLesion/PeTu#24 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[FEATURE] Cite final Paper Open

enhancement

BrainLesion/GlioMODA#16 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[BUG] Error 400 when trying to download the weights Open

bug

BrainLesion/GlioMODA#17 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[FEATURE] citation reminder Open

enhancement

BrainLesion/auxiliary#45 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[feature request] wholistic tutorial showing preprocessing and segmentation with AURORA Open

documentation enhancement good first issue

BrainLesion/tutorials#24 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 14, 2026
[feature request] nb viewer buttons Open

documentation enhancement good first issue help wanted

BrainLesion/tutorials#64 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[feature request] panoptica config tutorial should show actual yml configs Open

documentation enhancement

BrainLesion/tutorials#65 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Adding tutorials to MAIA Workspace Open

question

BrainLesion/tutorials#74 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 14, 2026
[BUG] preprocessing tutorials are outdated Open

bug

BrainLesion/tutorials#75 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[FEATURE] document data requirements Open

enhancement

BrainLesion/AURORA#57 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Support for instance proposals (bounding boxes) Open

enhancement

BrainLesion/panoptica#88 · 1 comment · 1 reaction · 1 assignee · Indexed Sep 14, 2026
Object Detection Open

enhancement metric

BrainLesion/panoptica#152 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 14, 2026
More fluent pipeline Open

enhancement metric

BrainLesion/panoptica#154 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
[FEATURE] aggregrated global evaluations Open

enhancement

BrainLesion/panoptica#168 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[FEATURE] Metric system Overhaul Open

enhancement metric

BrainLesion/panoptica#181 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
[FEATURE] more sophisticated unit tests also covering edge cases Open

enhancement

BrainLesion/panoptica#191 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[FEATURE] Easy to use tutorial for multiple classes Open

documentation enhancement tutorial

BrainLesion/panoptica#195 · 6 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[BUG] Currently breaking on Colab because of a potential colab issue: `ModuleNotFoundError: No module named 'numpy.strings'` Open

bug wontfix

BrainLesion/panoptica#211 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[DISCUSSION] How to setup `set_to_binary` in label groups. Open

BrainLesion/panoptica#219 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[FEATURE] Robust and Reliable Ranking Open

enhancement

BrainLesion/panoptica#224 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[FEATURE] Expanding visual unit tests Open

enhancement

BrainLesion/panoptica#226 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[FEATURE] cupy-based CCA Open

enhancement

BrainLesion/panoptica#232 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[FEATURE] class MaxBipartiteMatching(InstanceMatchingAlgorithm) cannot handle many-to-one Open

enhancement

BrainLesion/panoptica#236 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
REFACTOR PLAN Open

BrainLesion/panoptica#248 · 1 comment · 1 reaction · 0 assignees · Indexed Sep 14, 2026
[FEATURE] Swap module-level locks for an OS-level file lock Open

enhancement

BrainLesion/panoptica#261 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 14, 2026
[FEATURE] Report predicted instances Open

enhancement

BrainLesion/panoptica#267 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
[FEATURE] PanopticaStatistic object can derive ranges like quantiles based on group and metric Open

enhancement

BrainLesion/panoptica#286 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[FEATURE] unifying naming/naming convention of metrics Open

enhancement

BrainLesion/panoptica#289 · 0 comments · 0 reactions · 2 assignees · Indexed Sep 14, 2026
[FEATURE] Reproducibility Open

enhancement

BrainLesion/panoptica#294 · 5 comments · 1 reaction · 0 assignees · Indexed Sep 14, 2026
[FEATURE] Support for Diffusion-weighted Imaging Open

enhancement

BrainLesion/preprocessing#99 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[FEATURE] evaluate reorient Open

enhancement

BrainLesion/preprocessing#110 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[FEATURE] Make cuda/gpu optional Open

enhancement

BrainLesion/preprocessing#117 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[FEATURE] evaluate config file inputs with typechecking - consider YML config files for preprocessing Open

enhancement

BrainLesion/preprocessing#145 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[FEATURE] (MNI) atlas based defacing and BET Open

enhancement

BrainLesion/preprocessing#146 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[FEATURE] consider enabling n4 corrected and "raw" outputs in one pass Open

enhancement

BrainLesion/preprocessing#147 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[BUG] Potential wrong edge_mask calculation and out-of-range indexing issues with QuickShear defacing Open

bug

BrainLesion/preprocessing#167 · 6 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
[BUG] Zenodo api error response not saved nor displayed Open

bug

BrainLesion/preprocessing#169 · 7 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[FEATURE] modality-specific minima definitions for BET and defacing Open

enhancement

BrainLesion/preprocessing#174 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 14, 2026
[BUG] Cannot specify non-default interpolator for ANTsRegistrator Open

bug

BrainLesion/preprocessing#177 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[FEATURE] computation time and RAM monitoring Open

enhancement

BrainLesion/preprocessing#185 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[BUG] cannot import ANTSRegistrator Open

bug

BrainLesion/preprocessing#188 · 0 comments · 1 reaction · 2 assignees · Indexed Sep 14, 2026
[BUG] HTTP error responses from Zenodo bypass the "use local copy" fallback Open

bug

BrainLesion/preprocessing#190 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[FEATURE] Kubernetes support Open

enhancement

BrainLesion/BraTS#113 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
[FEATURE] documentation of challenge-specific preprocessing requirements Open

documentation enhancement

BrainLesion/BraTS#115 · 5 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
[FEATURE] integrate segmentation baselines from mehdi and Zhifan Open

enhancement

BrainLesion/BraTS#116 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
[FEATURE] Add the solution from the BraTS-ISBI GoAT 2024 Open

enhancement

BrainLesion/BraTS#135 · 6 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
[FEATURE] PermRanker Open

enhancement

BrainLesion/BraTS#141 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 14, 2026

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