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    • A repository containing a pipeline for teaching fine-tuning pipeline of 3D-EM segmentation models. Used in the ZooCell meeting at Naples, April 2026.
      Jupyter Notebook
      GNU General Public License v3.0
      1000Updated Apr 17, 2026Apr 17, 2026
    • panseg

      Public
      A tool for cell instance aware segmentation in densely packed 3D volumetric images
      Python
      MIT License
      42125321Updated Apr 13, 2026Apr 13, 2026
    • plant-seg

      Public
      PlantSeg is now PanSeg! Please head over to the new repo! This is an archive of the old version.
      Python
      MIT License
      0000Updated Mar 26, 2026Mar 26, 2026
    • Jupyter Notebook
      0100Updated Mar 11, 2026Mar 11, 2026
    • Guides and code for 3D nuclear instance segmentation
      Python
      MIT License
      32300Updated Dec 2, 2025Dec 2, 2025
    • Experiments related to finding the source of tiling artifacts in the segmentation pipelines based on the sliding window inference
      Jupyter Notebook
      0310Updated Oct 21, 2025Oct 21, 2025
    • bio-monai

      Public
      Additional data readers to use Monai for biological image analysis
      Python
      0000Updated Oct 21, 2025Oct 21, 2025
    • Kreshuk Lab's EMBL EIPP predoc course teaching material, each branch keeps the record of a specific season
      Jupyter Notebook
      2300Updated Oct 18, 2025Oct 18, 2025
    • Materials for the EMBL Deep Learning course
      Jupyter Notebook
      7600Updated Sep 22, 2025Sep 22, 2025
    • Software to control the Cryo Super-Resolution Light Microscope.
      Python
      GNU General Public License v3.0
      0000Updated Sep 11, 2025Sep 11, 2025
    • A rust implementation of bioimage spec parser
      Rust
      MIT License
      3260Updated Sep 5, 2025Sep 5, 2025
    • DINOv2 + linear classifier
      Python
      0000Updated Jun 29, 2025Jun 29, 2025
    • hylfm-net

      Public
      Python
      MIT License
      31401Updated Mar 13, 2025Mar 13, 2025
    • Jupyter Notebook
      0310Updated Jan 13, 2025Jan 13, 2025
    • EMBL Deep Learning course 2019 exercises and materials
      Jupyter Notebook
      MIT License
      8610Updated Aug 13, 2024Aug 13, 2024
    • spoco

      Public
      PyTorch implementation of SPOCO
      Python
      73311Updated Aug 3, 2024Aug 3, 2024
    • 3D segmentation of nuclei (fixed) and cells (live) of the developing mouse embryo
      Python
      1600Updated Jul 23, 2024Jul 23, 2024
    • Python
      0000Updated Jul 14, 2024Jul 14, 2024
    • List of tools for creating ground truth annotations for 3D data
      0200Updated Mar 26, 2024Mar 26, 2024
    • EMBL Deep Learning course 2023 exercises and materials
      Jupyter Notebook
      5613Updated Feb 28, 2024Feb 28, 2024
    • .github

      Public
      Kreshuk Group - Machine learning for bioimage analysis
      0200Updated May 19, 2023May 19, 2023
    • MorphoFeatures code and data
      Python
      GNU General Public License v3.0
      32210Updated May 4, 2023May 4, 2023
    • Python package for common lab code
      MIT License
      0000Updated Feb 17, 2023Feb 17, 2023
    • Neuroclear is a deep-learning-based Python module to train a deep neural network for the task of applying super-resolution to degraded axial resolution in fluor…
      Jupyter Notebook
      Apache License 2.0
      1000Updated Feb 14, 2023Feb 14, 2023
    • torch-em

      Public
      Deep-learning based semantic and instance segmentation for 3D Electron Microscopy and other bioimage analysis problems based on pytorch.
      Python
      MIT License
      31000Updated Feb 10, 2023Feb 10, 2023
    • Python
      0100Updated Nov 16, 2022Nov 16, 2022
    • Checking reward functions for lines and circles with line and circle data.
      Jupyter Notebook
      0000Updated Jul 30, 2022Jul 30, 2022
    • Jupyter Notebook
      MIT License
      1100Updated Apr 24, 2022Apr 24, 2022
    • Experiments for unsupervised pixel embeddings
      Python
      MIT License
      0000Updated Mar 26, 2022Mar 26, 2022
    • Shallow2deep: Exploiting feature-based classifiers for domain adaptation in semantic segmentation
      Jupyter Notebook
      MIT License
      561300Updated Mar 8, 2022Mar 8, 2022
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