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36 repositories

micro-sam
Public
Segment Anything for Microscopy
segmentation cell-segmentation bioimage-analysis
segmentation cell-segmentation bioimage-analysis microscopy-images nuclei-segmentation napari segment-anything mitochondria-segmentation micro-sam
Jupyter Notebook
•
MIT License
•105•693•51•18•Updated Jun 22, 2026Jun 22, 2026
bioimage-py
Public
Efficient, parallel, and distributed implementation of image analysis and segmentation functionality
Python
•
MIT License
•1•1•0•0•Updated Jun 21, 2026Jun 21, 2026
faket-polnet
Public
Python
•0•0•1•0•Updated Jun 17, 2026Jun 17, 2026
czii-protein-challenge
Public
Python
•1•1•0•0•Updated Jun 17, 2026Jun 17, 2026
cochlea-net
Public
Deep learning-based image analysis for cochleae imaged in light-sheet microscopy
Python
•1•6•12•3•Updated Jun 17, 2026Jun 17, 2026
bioimage-cpp
Public
Image analysis and segmentaton functionality in C++ with minimal python bindings
Python
•
MIT License
•1•2•0•0•Updated Jun 16, 2026Jun 16, 2026
computational-cell-analytics
Public
General resources and wiki of the Computational Cell Analytics Lab @ Uni Göttingen
Python
•0•2•0•0•Updated Jun 16, 2026Jun 16, 2026
synapse-net
Public
Reconstruction of synaptic structures in electron microscopy
Python
•
MIT License
•3•12•11•9•Updated Jun 15, 2026Jun 15, 2026
polnet-synaptic
Public
Generates synthetic datasets for Cryo-Electron Tomography
Python
•
Other
•14•1•0•0•Updated Jun 14, 2026Jun 14, 2026
micro_sam-feedstock
Public
A conda-smithy repository for micro_sam.
BSD 3-Clause "New" or "Revised" License
•5•0•0•0•Updated Jun 10, 2026Jun 10, 2026
peft-sam
Public
Parameter Efficient Fine-Tuning of Segment Anything Model
sam medical-imaging segmentation
sam medical-imaging segmentation microscopy peft finetuning segment-anything qlora micro-sam medico-sam
Python
•
MIT License
•3•35•0•0•Updated Jun 6, 2026Jun 6, 2026
medico-sam
Public
Segment Anything for Medical Imaging
sam medical-imaging segmentation
sam medical-imaging segmentation semantic-segmentation medical-image-segmentation interactive-segmentation segment-anything medico-sam
Python
•
MIT License
•2•31•1•0•Updated Jun 6, 2026Jun 6, 2026
patho-sam
Public
Segment Anything for Histopathology
sam segmentation wsi
sam segmentation wsi histopathology nuclei-segmentation segment-anything
Python
•
MIT License
•7•66•3•1•Updated Jun 6, 2026Jun 6, 2026
oct-sam
Public
Python
•0•0•2•0•Updated May 22, 2026May 22, 2026
ihc-pathosam
Public
Python
•0•1•3•0•Updated May 9, 2026May 9, 2026
segmentation-measurement-tool
Public
Segmentation meaurement and analys in the command line and napari
Python
•
MIT License
•0•0•7•1•Updated May 7, 2026May 7, 2026
phylogenetics-tutorial
Public
A simple introduction to computational phylogenetics
Jupyter Notebook
•
MIT License
•0•0•0•0•Updated May 1, 2026May 1, 2026
simulation-main
Public
Integrated pipeline for cryo-ET data simulation with PolNet and FakET.
Shell
•0•1•0•0•Updated Apr 20, 2026Apr 20, 2026
flamingo-scripts
Public
Scripts for data analysis of flamingo data
Python
•0•0•0•0•Updated Mar 9, 2026Mar 9, 2026
dl-for-micro
Public
Course and exercises on deep learning for microscopy image analysis
Jupyter Notebook
•
MIT License
•0•23•6•0•Updated Nov 25, 2025Nov 25, 2025
pdo_genetic_analysis
Public
Jupyter Notebook
•0•0•0•0•Updated Oct 19, 2025Oct 19, 2025
computational-cell-analytics.github.io
Public
HTML
•
MIT License
•0•1•0•0•Updated Oct 15, 2025Oct 15, 2025
stacc
Public
Python
•0•3•2•0•Updated Jul 23, 2025Jul 23, 2025
Probabilistic-Domain-Adaptation
Public
Probabilistic Domain Adaptation for Biomedical Image Segmentation
deep-learning segmentation electron-microscopy
deep-learning segmentation electron-microscopy domain-adaptation pseudo-label lung-xray probabilistic-unet livecell
Python
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MIT License
•0•6•0•0•Updated Jul 4, 2025Jul 4, 2025
.github
Public
0•0•0•0•Updated May 24, 2025May 24, 2025
spotiflow_microsam
Public
SpotiFlow x Segment Anything for Microscopy
segmentation microscopy spot-detection
segmentation microscopy spot-detection segment-anything micro-sam spotiflow
Jupyter Notebook
•0•1•0•0•Updated Feb 24, 2025Feb 24, 2025
vimunet-benchmarking
Public
Benchmarking nnU-Netv2 and U-Mamba for Biomedical Segmentation
Python
•1•0•1•0•Updated Jan 3, 2025Jan 3, 2025
protein-detection
Public
0•0•0•0•Updated Dec 13, 2024Dec 13, 2024
user-study-v3
Public
Python
•1•1•0•0•Updated Nov 14, 2024Nov 14, 2024
oc-sync
Public
Sync ownCloud
Python
•
MIT License
•0•0•0•0•Updated Mar 20, 2024Mar 20, 2024

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computational-cell-analytics

All

All

36 repositories

micro-sam

bioimage-py

faket-polnet

czii-protein-challenge

cochlea-net

bioimage-cpp

computational-cell-analytics

synapse-net

polnet-synaptic

micro_sam-feedstock

peft-sam

medico-sam

patho-sam

oct-sam

ihc-pathosam

segmentation-measurement-tool

phylogenetics-tutorial

simulation-main

flamingo-scripts

dl-for-micro

pdo_genetic_analysis

computational-cell-analytics.github.io

stacc

Probabilistic-Domain-Adaptation

.github

spotiflow_microsam

vimunet-benchmarking

protein-detection

user-study-v3

oc-sync

All

All

Repositories list

36 repositories