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  1. panseg panseg Public

    A tool for cell instance aware segmentation in densely packed 3D volumetric images

    Python 130 42

  2. spoco spoco Public

    PyTorch implementation of SPOCO

    Python 34 7

  3. MorphoFeatures MorphoFeatures Public

    MorphoFeatures code and data

    Python 23 3

  4. go-nuclear go-nuclear Public

    Guides and code for 3D nuclear instance segmentation

    Python 23 4

  5. hylfm-net hylfm-net Public

    Python 14 3

  6. EMBL-Deep-Learning-course-2023- EMBL-Deep-Learning-course-2023- Public

    EMBL Deep Learning course 2023 exercises and materials

    Jupyter Notebook 7 5

Repositories

Showing 10 of 49 repositories
  • image-matchmaker Public

    Tool for segmentation-based deformable registration

    kreshuklab/image-matchmaker's past year of commit activity
    Python 1 0 5 0 Updated Sep 11, 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 130 MIT 42 22 (1 issue needs help) 0 Updated Sep 11, 2026
  • model_ranking Public
    kreshuklab/model_ranking's past year of commit activity
    Python 1 0 0 0 Updated Sep 11, 2026
  • MorphoFeatures Public

    MorphoFeatures code and data

    kreshuklab/MorphoFeatures's past year of commit activity
    Python 23 GPL-3.0 3 1 0 Updated Sep 10, 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 0 GPL-3.0 1 0 0 Updated May 29, 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 2 MIT 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 23 MIT 4 0 0 Updated Dec 2, 2025
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