MIC-DKFZ/nnUNet

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Stars: 8.9k
Forks: 2.5k
Open beginner issues: 0
Indexed issues: 71

Dominant language: Python
License: Apache-2.0
Last GitHub push: Sep 14, 2026
Latest indexed: Sep 20, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

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71 open issues indexed

[Feature Request]: tiff compression of saved predictions Open

enhancement

MIC-DKFZ/nnUNet#3069 · 1 comment · 1 assignee · Opened Sep 16, 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
--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
Segmentation fault (core dumped) Open

bug needs-maintainer needs-repro

MIC-DKFZ/nnUNet#3051 · 3 comments · 1 assignee · Opened Jul 7, 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
[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
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
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
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
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
[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
nnUNet comparison to MedSegX Open

MIC-DKFZ/nnUNet#2904 · 1 comment · 1 assignee · Opened Sep 12, 2025
nnUNet_plan_and_preprocess: error: unrecognized arguments: -d Open

MIC-DKFZ/nnUNet#2875 · 1 comment · 1 assignee · Opened Jul 23, 2025
Background workers not alive / EOF error / no CUDA GPU available Open

MIC-DKFZ/nnUNet#2825 · 4 comments · 2 assignees · Opened May 28, 2025
Validation files not being saved Open

MIC-DKFZ/nnUNet#2811 · 9 comments · 1 assignee · Opened May 16, 2025
unable to pick up where i left off in training Broken pipe error. Slurm Open

MIC-DKFZ/nnUNet#2799 · 1 comment · 1 assignee · Opened May 7, 2025
no postprocessing.pkl Open

question

MIC-DKFZ/nnUNet#2789 · 3 comments · 1 assignee · Opened Apr 27, 2025
The validation mask in validation and running an inference it's not similar Open

MIC-DKFZ/nnUNet#2787 · 9 comments · 1 assignee · Opened Apr 24, 2025
The difference with Original U-Net Open

MIC-DKFZ/nnUNet#2776 · 2 comments · 1 assignee · Opened Apr 7, 2025
Unable to plot network architecture Open

MIC-DKFZ/nnUNet#2772 · 4 comments · 2 reactions · 1 assignee · Opened Apr 4, 2025
Training RuntimeError: One or more background workers are no longer alive Open

MIC-DKFZ/nnUNet#2769 · 9 comments · 1 assignee · Opened Apr 2, 2025
How to sepearte Prediction procedure into two parts？ Open

MIC-DKFZ/nnUNet#2757 · 1 comment · 1 assignee · Opened Mar 28, 2025
Training fails with TypeError: full() received an invalid combination of arguments Open

MIC-DKFZ/nnUNet#2735 · 5 comments · 1 assignee · Opened Mar 13, 2025
Adding a new `nnUNetTrainer` variant for extensive data augmentations Open

MIC-DKFZ/nnUNet#2733 · 13 comments · 11 reactions · 1 assignee · Opened Mar 11, 2025
ValueError: mmap length is greater than file size for 2d models Open

MIC-DKFZ/nnUNet#2732 · 2 comments · 1 assignee · Opened Mar 11, 2025
TensorRT deployment Open

MIC-DKFZ/nnUNet#2706 · 1 comment · 1 assignee · Opened Feb 18, 2025
Pickling issue- Can't pickle local object 'nnUNetTrainerV2.initialize_network.<locals>.<lambda>' Open

MIC-DKFZ/nnUNet#2671 · 6 comments · 1 assignee · Opened Jan 19, 2025
there are so many question like "RuntimeError: Some background workers are no longer alive", BUT no one can resove it Open

MIC-DKFZ/nnUNet#2659 · 5 comments · 1 assignee · Opened Dec 28, 2024
Use custom models and custom data loading functions Open

MIC-DKFZ/nnUNet#2646 · 1 comment · 1 assignee · Opened Dec 17, 2024
Ensemble of different custom models Open

MIC-DKFZ/nnUNet#2642 · 1 comment · 1 assignee · Opened Dec 13, 2024
Model output NaN Open

MIC-DKFZ/nnUNet#2603 · 1 comment · 3 reactions · 1 assignee · Opened Nov 17, 2024
preprocessing Open

MIC-DKFZ/nnUNet#2592 · 1 comment · 1 assignee · Opened Nov 9, 2024
Overlapping segmentation using png input and png label Open

MIC-DKFZ/nnUNet#2579 · 1 comment · 1 reaction · 1 assignee · Opened Nov 2, 2024
Error when using DDP and deep_supervision=False Open

MIC-DKFZ/nnUNet#2571 · 8 comments · 1 assignee · Opened Oct 29, 2024
Ignore Labels for 2D images Open

MIC-DKFZ/nnUNet#2567 · 2 comments · 1 assignee · Opened Oct 24, 2024
Training. Torch Error? Open

MIC-DKFZ/nnUNet#2533 · 2 comments · 1 reaction · 1 assignee · Opened Oct 8, 2024
overfitting and low dice Open

MIC-DKFZ/nnUNet#2512 · 1 comment · 1 assignee · Opened Sep 20, 2024

MIC-DKFZ/nnUNet

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