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kreshuklab

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Kreshuk Group - Machine learning for bioimage analysis

The Kreshuk group develops machine learning-based methods and tools for automatic segmentation, classification and analysis of biological images.

Teaching material

An image segemntation pipeline for immunofluorescence images of COVID-infected cells (2D)

Popular repositories Loading

panseg pansegPublic
A tool for cell instance aware segmentation in densely packed 3D volumetric images
Python 130 42
spoco spocoPublic
PyTorch implementation of SPOCO
Python 33 7
MorphoFeatures MorphoFeaturesPublic
MorphoFeatures code and data
Python 23 3
go-nuclear go-nuclearPublic
Guides and code for 3D nuclear instance segmentation
Python 23 4
hylfm-net hylfm-netPublic
Python 14 3
EMBL-Deep-Learning-course-2023- EMBL-Deep-Learning-course-2023-Public
EMBL Deep Learning course 2023 exercises and materials
Jupyter Notebook 7 5

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Showing 10 of 49 repositories

model_ranking Public
kreshuklab/model_ranking's past year of commit activity
Python 1 0 0 0 Updated Aug 10, 2026
image-matchmaker Public
Tool for segmentation-based deformable registration
kreshuklab/image-matchmaker's past year of commit activity
Python 1 0 7 2 Updated Aug 8, 2026
panseg Public
A tool for cell instance aware segmentation in densely packed 3D volumetric images
kreshuklab/panseg's past year of commit activity
Python 130MIT 42 29 (2 issues need help) 2 Updated Aug 3, 2026
DINOv2_classifier Public
DINOv2 + linear classifier
kreshuklab/DINOv2_classifier's past year of commit activity
Python 0 0 0 0 Updated Aug 3, 2026
diff_detect Public
Difference Detective (Lab day 2026)
kreshuklab/diff_detect's past year of commit activity
Python 0 0 0 0 Updated Jul 10, 2026
zoocell_seg_ws_2026 Public
A repository containing a pipeline for teaching fine-tuning pipeline of 3D-EM segmentation models. Used in the ZooCell meeting at Naples, April 2026.
kreshuklab/zoocell_seg_ws_2026's past year of commit activity
Jupyter Notebook 0GPL-3.0 1 0 0 Updated May 29, 2026
MorphoFeatures Public
MorphoFeatures code and data
kreshuklab/MorphoFeatures's past year of commit activity
Python 23GPL-3.0 3 1 0 Updated May 11, 2026
plant-seg Public
PlantSeg is now PanSeg! Please head over to the new repo! This is an archive of the old version.
kreshuklab/plant-seg's past year of commit activity
Python 2MIT 0 0 0 Updated Mar 26, 2026
CRank-Consistency_based_ranking Public
kreshuklab/CRank-Consistency_based_ranking's past year of commit activity
Jupyter Notebook 1 0 0 0 Updated Mar 11, 2026
go-nuclear Public
Guides and code for 3D nuclear instance segmentation
kreshuklab/go-nuclear's past year of commit activity
Python 23MIT 4 0 0 Updated Dec 2, 2025

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