Owner

MIC-DKFZ

13 indexed repositories · View on GitHub

nnUNet

Python · 8897 stars
nnInteractive
nnInteractive is a framework for 3D interactive segmentation, supporting intuitive prompts like points, scribbles, bounding boxes, and la...

Python · 493 stars
VoxTell
Free-Text Promptable Universal 3D Medical Image Segmentation

Python · 267 stars
dynamic-network-architectures

Python · 159 stars
napari-nninteractive
nnInteractive plugin for Napari - nnInteractive is a framework for 3D interactive segmentation, supporting intuitive prompts like points,...

Python · 123 stars
LesionLocator
LesionLocator is a framework for zero-shot lesion segmentation and longitudinal tumor tracking in 3D full-body imaging.

Python · 112 stars
niicat
This is a tool to quickly preview nifti images on the terminal

Python · 75 stars
MultiTalent
Implemention of the Paper "MultiTalent: A Multi-Dataset Approach to Medical Image Segmentation"

Python · 71 stars
nnLandmark

Python · 53 stars
Longitudinal4DMed

Python · 19 stars
Longitudinal-Difference-Weighting
Longitudinal Segmentation of MS Lesions via Temporal Difference Weighting

Python · 13 stars
radioactive

Python · 12 stars
napari-nifti

Python · 5 stars

Beginner friendly Everything

Open All

Question: Best practices for missing labels (ignore_label) and reducing training epochs Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

MIC-DKFZ/nnLandmark#8 · 1 comment · Opened Sep 18, 2026
[Feature Request]: tiff compression of saved predictions Open

enhancement

MIC-DKFZ/nnUNet#3069 · 1 comment · 1 assignee · Opened Sep 16, 2026
Custom trainer produces 5 output channels during inference instead of 4 Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

MIC-DKFZ/nnLandmark#7 · 1 comment · Opened Sep 13, 2026
TypeError: nnUNetTrainer.__init__() takes from 5 to 6 positional arguments but 7 were given Open

question

MIC-DKFZ/nnUNet#3066 · 2 comments · 1 assignee · Opened Sep 11, 2026
Race condition in nnUNetTrainer.do_split(): concurrent trainings can read a partially written splits_final.json Open

bug needs-maintainer

MIC-DKFZ/nnUNet#3064 · 1 comment · 1 assignee · Opened Sep 9, 2026
Discussion: batched GPU data augmentation Open

MIC-DKFZ/nnUNet#3063 · 1 assignee · Opened Sep 7, 2026
Target time dropped by process_batch_non_zero Open

Difficulty 3/5 1-2 days Newbie friendliness 72/100

MIC-DKFZ/Longitudinal4DMed#1 · Opened Aug 11, 2026
--val --val_best fails when checkpoint_final is missing Open

bug needs-maintainer

MIC-DKFZ/nnUNet#3056 · 2 comments · 1 assignee · Opened Jul 20, 2026
ignore index included in foreground when calculating dataset fingerprint Open

bug needs-maintainer

MIC-DKFZ/nnUNet#3055 · 1 comment · 1 assignee · Opened Jul 19, 2026
predict_from_raw_data.py __main__ block hardcodes Dataset004_Hippocampus (v2.8.1) Open

bug needs-maintainer

MIC-DKFZ/nnUNet#3052 · 3 comments · 1 assignee · Opened Jul 13, 2026
Prediction visualization issue Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

MIC-DKFZ/nnLandmark#6 · 4 comments · Opened Jul 11, 2026
Segmentation fault (core dumped) Open

bug needs-maintainer needs-repro

MIC-DKFZ/nnUNet#3051 · 3 comments · 1 assignee · Opened Jul 7, 2026
Adding multiple scribbles at once? Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

MIC-DKFZ/napari-nninteractive#35 · Opened Jul 6, 2026
Discussion: optional RankSEG-style decoding support for nnU-Net inference Open

MIC-DKFZ/nnUNet#3050 · 5 comments · 4 reactions · 1 assignee · Opened Jul 4, 2026
All classes climb to EMA pseudo-Dice ~0.06 by epoch ~55, then collapse back to ~0 by epoch 1000 (extremely sparse multi-class MRI) Open

MIC-DKFZ/nnUNet#3048 · 2 comments · 1 assignee · Opened Jul 2, 2026
Error when clicking [Export] Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

MIC-DKFZ/napari-nninteractive#33 · 2 comments · Opened Jul 2, 2026
OME-Zarr compatibility Open

Difficulty 3/5 1-2 days Newbie friendliness 55/100

MIC-DKFZ/napari-nninteractive#32 · 2 comments · Opened Jul 2, 2026
Do not override existing labels when writing segmentations into the same label mask Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

MIC-DKFZ/napari-nninteractive#31 · 4 comments · Opened Jul 2, 2026
Possible argument-order bug in nnUNetDataLoader3D_MTall.get_bbox call causing foreground-centered crops Open

Difficulty 3/5 1-2 days Newbie friendliness 55/100

MIC-DKFZ/MultiTalent#27 · 4 comments · Opened Jun 29, 2026
"Not found" error on ITK Snap (connecting to remote server) Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

MIC-DKFZ/nnInteractive#38 · 1 comment · Opened Jun 4, 2026
LesionLocator Docker Image Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

MIC-DKFZ/LesionLocator#13 · 1 comment · Opened May 19, 2026
Is there any functionality to classify a landmark as undefined? Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

MIC-DKFZ/nnLandmark#4 · 1 comment · Opened May 5, 2026
loss design Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

MIC-DKFZ/nnLandmark#3 · 1 comment · Opened Apr 29, 2026
Deep Supervision for Landmark Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

MIC-DKFZ/nnLandmark#2 · 1 comment · Opened Apr 24, 2026
[Feature Request] Optional Visualization / Debug Mode for Preprocessing and Training. Open

feature request

MIC-DKFZ/nnUNet#3023 · 2 comments · 1 assignee · Opened Apr 20, 2026
MedNeXt-v2 Resources Open

question

MIC-DKFZ/nnUNet#3022 · 3 comments · 2 assignees · Opened Apr 20, 2026
Advice on training strategy: Large dataset (>6000 images), Open

question

MIC-DKFZ/nnUNet#3010 · 3 comments · 1 assignee · Opened Apr 2, 2026
Is there any plan to include the nnInteractive into this benchchmark? Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

MIC-DKFZ/radioactive#3 · 4 comments · Opened Apr 1, 2026
metric is best when it is smaller Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

MIC-DKFZ/nnLandmark#1 · 6 comments · Opened Apr 1, 2026
ReXGroundingCT data Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

MIC-DKFZ/VoxTell#11 · 6 comments · Opened Mar 26, 2026
Error during preprocessing with latest version (2.6.4), fixed by downgrading Open

MIC-DKFZ/nnUNet#3003 · 10 comments · 1 assignee · Opened Mar 18, 2026
Clarification regarding community contributions and pending PRs Open

MIC-DKFZ/nnUNet#2997 · 1 comment · 1 assignee · Opened Mar 8, 2026
Support for importing existing labels as positive/negative scribbles Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

MIC-DKFZ/napari-nninteractive#28 · 2 comments · Opened Feb 12, 2026
Advice on integrating custom intensity augmentation into nnU-Net Open

question

MIC-DKFZ/nnUNet#2986 · 5 comments · 1 assignee · Opened Feb 6, 2026
model archetecture Open

MIC-DKFZ/nnUNet#2984 · 1 comment · 1 assignee · Opened Feb 3, 2026
advice on creating ground-truth Open

MIC-DKFZ/nnUNet#2981 · 1 comment · 1 assignee · Opened Jan 23, 2026
forum.image.sc Open

Difficulty 2/5 1-3 hours Newbie friendliness 25/100

MIC-DKFZ/nnInteractive#35 · 2 comments · Opened Jan 16, 2026
Low dice on test data only Open

MIC-DKFZ/nnUNet#2968 · 2 comments · 1 assignee · Opened Dec 23, 2025
Release MedNeXt-v2 on Hugging Face Open

MIC-DKFZ/nnUNet#2966 · 3 comments · 2 assignees · Opened Dec 22, 2025
CUDA Out of Memory during 3d_fullres inference on RTX 5090 (32 GB VRAM, Windows/WDDM) Open

MIC-DKFZ/nnUNet#2963 · 4 comments · 1 reaction · 1 assignee · Opened Dec 17, 2025
Unable to export nnUNetPredictor for Triton Deployment Open

question

MIC-DKFZ/nnUNet#2954 · 2 comments · 1 assignee · Opened Nov 30, 2025
Time-line for code releasre Open

Difficulty 5/5 Over a week Newbie friendliness 5/100

MIC-DKFZ/VoxTell#2 · 5 comments · Opened Nov 18, 2025
Warning: No spacing information found in dataset properties. Using default spacing [1. 1. 1.] Open

MIC-DKFZ/nnUNet#2937 · 1 comment · 1 assignee · Opened Nov 5, 2025
Why doesn't it work well on my local machine? Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

MIC-DKFZ/napari-nninteractive#25 · 1 comment · Opened Oct 26, 2025
[Bug] Validation fails with OOM on GPU and ArrayMemoryError on CPU fallback (nnU-Net v2, Windows 10, RTX 3060, 16GB RAM) Open

MIC-DKFZ/nnUNet#2912 · 12 comments · 1 assignee · Opened Sep 29, 2025
ITK-SNAP 4.4 with nnInteractive model Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

MIC-DKFZ/nnInteractive#27 · 1 comment · Opened Sep 16, 2025
nnUNet comparison to MedSegX Open

MIC-DKFZ/nnUNet#2904 · 1 comment · 1 assignee · Opened Sep 12, 2025
prompt Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

MIC-DKFZ/nnInteractive#26 · 1 comment · Opened Sep 10, 2025
Training code availability and how to train on my own dataset Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

MIC-DKFZ/LesionLocator#9 · 1 comment · 1 reaction · Opened Sep 4, 2025
Undo interaction result Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

MIC-DKFZ/nnInteractive#24 · 2 comments · 1 reaction · Opened Aug 27, 2025

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