computational-cell-analytics

All

26 repositories

micro-sam
Public
Segment Anything for Microscopy
segmentation cell-segmentation bioimage-analysis microscopy-images nuclei-segmentation napari segment-anything mitochondria-segmentation micro-sam
Jupyter Notebook
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MIT License
•87•622•61•18•Updated Dec 10, 2025Dec 10, 2025
cochlea-net
Public
Deep learning-based image analysis for cochleae imaged in light-sheet microscopy
Python
•1•5•9•3•Updated Dec 9, 2025Dec 9, 2025
synapse-net
Public
Reconstruction of synaptic structures in electron microscopy
Python
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MIT License
•3•11•11•10•Updated Nov 27, 2025Nov 27, 2025
dl-for-micro
Public
Course and exercises on deep learning for microscopy image analysis
Jupyter Notebook
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MIT License
•0•21•6•0•Updated Nov 25, 2025Nov 25, 2025
czii-protein-challenge
Public
Python
•1•1•0•0•Updated Nov 20, 2025Nov 20, 2025
medico-sam
Public
Segment Anything for Medical Imaging
sam medical-imaging segmentation semantic-segmentation medical-image-segmentation interactive-segmentation segment-anything medico-sam
Python
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MIT License
•1•27•0•0•Updated Oct 20, 2025Oct 20, 2025
pdo_genetic_analysis
Public
Jupyter Notebook
•0•0•0•0•Updated Oct 19, 2025Oct 19, 2025
computational-cell-analytics.github.io
Public
HTML
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MIT License
•0•1•0•0•Updated Oct 15, 2025Oct 15, 2025
peft-sam
Public
Parameter Efficient Fine-Tuning of Segment Anything Model
sam medical-imaging segmentation microscopy peft finetuning segment-anything qlora micro-sam medico-sam
Python
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MIT License
•3•29•0•0•Updated Oct 8, 2025Oct 8, 2025
patho-sam
Public
Segment Anything for Histopathology
sam segmentation wsi histopathology nuclei-segmentation segment-anything
Python
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MIT License
•6•55•3•1•Updated Oct 8, 2025Oct 8, 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 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
micro_sam-feedstock
Public
A conda-smithy repository for micro_sam.
BSD 3-Clause "New" or "Revised" License
•5•0•0•0•Updated Jun 14, 2025Jun 14, 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 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
•0•1•0•0•Updated Nov 14, 2024Nov 14, 2024
oc-sync
Public
Sync ownCloud
Python
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MIT License
•0•0•0•0•Updated Mar 20, 2024Mar 20, 2024
pyseg_system
Public
De novo analysis for cryo-electron tomography
C
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Other
•5•0•0•0•Updated Oct 17, 2023Oct 17, 2023
staged-recipes
Public
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
Python
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BSD 3-Clause "New" or "Revised" License
•5.6k•0•0•0•Updated Oct 4, 2023Oct 4, 2023
samapi
Public
Segment Anything Model API
Python
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BSD 3-Clause "New" or "Revised" License
•19•0•0•0•Updated Sep 4, 2023Sep 4, 2023
qupath-extension-sam
Public
QuPath extension for Segment Anything Model (SAM)
Java
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GNU General Public License v3.0
•17•0•0•0•Updated Jul 5, 2023Jul 5, 2023
sv-analysis-hpc
Public
Prototypes for synaptic vesicle analysis on HPC
Python
•0•0•0•0•Updated May 31, 2023May 31, 2023
computational-cell-analytics
Public
General resources and wiki of the Computational Cell Analytics Lab @ Uni Göttingen
Python
•0•2•0•0•Updated May 30, 2023May 30, 2023
classical-cv-basics
Public
Slides for talk on the basics of classical computer vision
0•0•0•0•Updated Sep 8, 2022Sep 8, 2022