Repositories list

• patho-sam

  Public
  Segment Anything for Histopathology

  samsegmentationwsi+ 3

  samsegmentationwsihistopathologynuclei-segmentationsegment-anything

  Python

  •

  MIT License

  •77 forks•6363 stars•33 issues•11 pull request•Updated Apr 23, 2026Apr 23, 2026

• micro-sam

  Public
  Segment Anything for Microscopy

  segmentationcell-segmentationbioimage-analysis+ 6

  segmentationcell-segmentationbioimage-analysismicroscopy-imagesnuclei-segmentationnaparisegment-anythingmitochondria-segmentationmicro-sam

  Jupyter Notebook

  •

  MIT License

  •101101 forks•678678 stars•6262 issues•2020 pull requests•Updated Apr 23, 2026Apr 23, 2026

• czii-protein-challenge

  Public
  Python

  •11 fork•11 star•11 issue•00 pull requests•Updated Apr 23, 2026Apr 23, 2026

• synapse-net

  Public
  Reconstruction of synaptic structures in electron microscopy

  Python

  •

  MIT License

  •33 forks•1111 stars•1212 issues•1010 pull requests•Updated Apr 22, 2026Apr 22, 2026

• simulation-main

  Public
  Integrated pipeline for cryo-ET data simulation with PolNet and FakET.

  Shell

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• polnet-synaptic

  Public

  computational-cell-analytics/polnet-synaptic’s past year of commit activity
  Generates synthetic datasets for Cryo-Electron Tomography

  Python

  •

  Other

  •1414 forks•11 star•00 issues•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• cochlea-net

  Public
  Deep learning-based image analysis for cochleae imaged in light-sheet microscopy

  Python

  •11 fork•66 stars•1212 issues•33 pull requests•Updated Apr 20, 2026Apr 20, 2026

• faket-polnet

  Public
  Python

  •00 forks•00 stars•11 issue•00 pull requests•Updated Apr 16, 2026Apr 16, 2026

• ihc-pathosam

  Public
  Python

  •00 forks•11 star•11 issue•00 pull requests•Updated Apr 9, 2026Apr 9, 2026

• medico-sam

  Public
  Segment Anything for Medical Imaging

  sammedical-imagingsegmentation+ 5

  sammedical-imagingsegmentationsemantic-segmentationmedical-image-segmentationinteractive-segmentationsegment-anythingmedico-sam

  Python

  •

  MIT License

  •11 fork•2929 stars•11 issue•00 pull requests•Updated Mar 11, 2026Mar 11, 2026

• flamingo-scripts

  Public
  Scripts for data analysis of flamingo data

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 9, 2026Mar 9, 2026

• dl-for-micro

  Public
  Course and exercises on deep learning for microscopy image analysis

  Jupyter Notebook

  •

  MIT License

  •00 forks•2323 stars•66 issues•00 pull requests•Updated Nov 25, 2025Nov 25, 2025

• pdo_genetic_analysis

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 19, 2025Oct 19, 2025

• computational-cell-analytics.github.io

  Public
  HTML

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Oct 15, 2025Oct 15, 2025

• peft-sam

  Public
  Parameter Efficient Fine-Tuning of Segment Anything Model

  sammedical-imagingsegmentation+ 7

  sammedical-imagingsegmentationmicroscopypeftfinetuningsegment-anythingqloramicro-sammedico-sam

  Python

  •

  MIT License

  •33 forks•3535 stars•00 issues•00 pull requests•Updated Oct 8, 2025Oct 8, 2025

• stacc

  Public
  Python

  •00 forks•33 stars•22 issues•00 pull requests•Updated Jul 23, 2025Jul 23, 2025

• Probabilistic-Domain-Adaptation

  Public
  Probabilistic Domain Adaptation for Biomedical Image Segmentation

  deep-learningsegmentationelectron-microscopy+ 5

  deep-learningsegmentationelectron-microscopydomain-adaptationpseudo-labellung-xrayprobabilistic-unetlivecell

  Python

  •

  MIT License

  •00 forks•66 stars•00 issues•00 pull requests•Updated Jul 4, 2025Jul 4, 2025

• micro_sam-feedstock

  Public
  A conda-smithy repository for micro_sam.

  BSD 3-Clause "New" or "Revised" License

  •55 forks•00 stars•00 issues•00 pull requests•Updated Jun 14, 2025Jun 14, 2025

• .github

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated May 24, 2025May 24, 2025

• spotiflow_microsam

  Public
  SpotiFlow x Segment Anything for Microscopy

  segmentationmicroscopyspot-detection+ 3

  segmentationmicroscopyspot-detectionsegment-anythingmicro-samspotiflow

  Jupyter Notebook

  •00 forks•11 star•00 issues•00 pull requests•Updated Feb 24, 2025Feb 24, 2025

• vimunet-benchmarking

  Public
  Benchmarking nnU-Netv2 and U-Mamba for Biomedical Segmentation

  Python

  •11 fork•00 stars•11 issue•00 pull requests•Updated Jan 3, 2025Jan 3, 2025

• protein-detection

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Dec 13, 2024Dec 13, 2024

• user-study-v3

  Public
  Python

  •11 fork•11 star•00 issues•00 pull requests•Updated Nov 14, 2024Nov 14, 2024

• oc-sync

  Public
  Sync ownCloud

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 20, 2024Mar 20, 2024

• pyseg_system

  Public
  De novo analysis for cryo-electron tomography

  C

  •

  Other

  •55 forks•00 stars•00 issues•00 pull requests•Updated Oct 17, 2023Oct 17, 2023

• staged-recipes

  Public
  A place to submit conda recipes before they become fully fledged conda-forge feedstocks

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •5.9k5.9k forks•00 stars•00 issues•00 pull requests•Updated Oct 4, 2023Oct 4, 2023

• samapi

  Public
  Segment Anything Model API

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •2323 forks•00 stars•00 issues•00 pull requests•Updated Sep 4, 2023Sep 4, 2023

• qupath-extension-sam

  Public
  QuPath extension for Segment Anything Model (SAM)

  Java

  •

  GNU General Public License v3.0

  •1717 forks•00 stars•00 issues•00 pull requests•Updated Jul 5, 2023Jul 5, 2023

• sv-analysis-hpc

  Public
  Prototypes for synaptic vesicle analysis on HPC

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 31, 2023May 31, 2023

• computational-cell-analytics

  Public
  General resources and wiki of the Computational Cell Analytics Lab @ Uni Göttingen

  Python

  •00 forks•22 stars•00 issues•00 pull requests•Updated May 30, 2023May 30, 2023