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    45 repositories

    • 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.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Apr 17, 2026Apr 17, 2026

    • panseg

      Public
      A tool for cell instance aware segmentation in densely packed 3D volumetric images
      bioinformaticsdeep-learningneural-network
      bioinformaticsdeep-learningneural-networksegmentationimage-segmentationunetbioimage-analysis
      Python
      •
      MIT License
      •42•125•32•1•Updated 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
      •0•0•0•0•Updated Mar 26, 2026Mar 26, 2026

    • CRank-Consistency_based_ranking

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Mar 11, 2026Mar 11, 2026

    • go-nuclear

      Public
      Guides and code for 3D nuclear instance segmentation
      instance-segmentationbioimage-analysis
      instance-segmentationbioimage-analysis
      Python
      •
      MIT License
      •3•23•0•0•Updated Dec 2, 2025Dec 2, 2025

    • no_tiling_artifacts

      Public
      Experiments related to finding the source of tiling artifacts in the segmentation pipelines based on the sliding window inference
      Jupyter Notebook
      •0•3•1•0•Updated Oct 21, 2025Oct 21, 2025

    • bio-monai

      Public
      Additional data readers to use Monai for biological image analysis
      Python
      •0•0•0•0•Updated Oct 21, 2025Oct 21, 2025

    • predoc-course

      Public
      Kreshuk Lab's EMBL EIPP predoc course teaching material, each branch keeps the record of a specific season
      Jupyter Notebook
      •2•3•0•0•Updated Oct 18, 2025Oct 18, 2025

    • teaching-dl-course-2022

      Public
      Materials for the EMBL Deep Learning course
      Jupyter Notebook
      •7•6•0•0•Updated Sep 22, 2025Sep 22, 2025

    • CryoSResCLEMcontrol

      Public
      Software to control the Cryo Super-Resolution Light Microscope.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 11, 2025Sep 11, 2025

    • bioimageio_rs

      Public
      A rust implementation of bioimage spec parser
      Rust
      •
      MIT License
      •3•2•6•0•Updated Sep 5, 2025Sep 5, 2025

    • DINOv2_classifier

      Public
      DINOv2 + linear classifier
      Python
      •0•0•0•0•Updated Jun 29, 2025Jun 29, 2025

    • hylfm-net

      Public
      Python
      •
      MIT License
      •3•14•0•1•Updated Mar 13, 2025Mar 13, 2025

    • ADL4IA-2025

      Public
      Jupyter Notebook
      •0•3•1•0•Updated Jan 13, 2025Jan 13, 2025

    • teaching-dl-course-2019

      Public
      EMBL Deep Learning course 2019 exercises and materials
      Jupyter Notebook
      •
      MIT License
      •8•6•1•0•Updated Aug 13, 2024Aug 13, 2024

    • spoco

      Public
      PyTorch implementation of SPOCO
      Python
      •7•33•1•1•Updated Aug 3, 2024Aug 3, 2024

    • mouse-embryo-seg

      Public
      3D segmentation of nuclei (fixed) and cells (live) of the developing mouse embryo
      Python
      •1•6•0•0•Updated Jul 23, 2024Jul 23, 2024

    • covid-if-2

      Public
      Python
      •0•0•0•0•Updated Jul 14, 2024Jul 14, 2024

    • 3D-GT-tools

      Public
      List of tools for creating ground truth annotations for 3D data
      0•2•0•0•Updated Mar 26, 2024Mar 26, 2024

    • EMBL-Deep-Learning-course-2023-

      Public
      EMBL Deep Learning course 2023 exercises and materials
      Jupyter Notebook
      •5•6•1•3•Updated Feb 28, 2024Feb 28, 2024

    • .github

      Public
      Kreshuk Group - Machine learning for bioimage analysis
      0•2•0•0•Updated May 19, 2023May 19, 2023

    • MorphoFeatures

      Public
      MorphoFeatures code and data
      Python
      •
      GNU General Public License v3.0
      •3•22•1•0•Updated May 4, 2023May 4, 2023

    • kreshuklab-utils

      Public
      Python package for common lab code
      MIT License
      •0•0•0•0•Updated Feb 17, 2023Feb 17, 2023

    • neuroclear

      Public
      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
      •1•0•0•0•Updated 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
      •31•0•0•0•Updated Feb 10, 2023Feb 10, 2023

    • sea-urchin-em-segmentation

      Public
      Python
      •0•1•0•0•Updated Nov 16, 2022Nov 16, 2022

    • rewardchecking

      Public
      Checking reward functions for lines and circles with line and circle data.
      Jupyter Notebook
      •0•0•0•0•Updated Jul 30, 2022Jul 30, 2022

    • Plantseg-Cellpose-Augmentation

      Public
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Apr 24, 2022Apr 24, 2022

    • unsup_pix_embed

      Public
      Experiments for unsupervised pixel embeddings
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 26, 2022Mar 26, 2022

    • shallow2deep

      Public
      Shallow2deep: Exploiting feature-based classifiers for domain adaptation in semantic segmentation
      Jupyter Notebook
      •
      MIT License
      •561•3•0•0•Updated Mar 8, 2022Mar 8, 2022
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