Repositories list

• czii-protein-challenge

  Public
  Python

  •0•0•0•0•Updated Feb 3, 2025Feb 3, 2025

• synapse-net

  Public
  Reconstruction of synaptic structures in electron microscopy

  Python

  •

  MIT License

  •1•7•4•5•Updated Feb 3, 2025Feb 3, 2025

• patho-sam

  Public
  Segment Anything for Histopathology

  samsegmentationhistopathology+ 2nuclei-segmentationsegment-anything

  Python

  •

  MIT License

  •0•2•3•0•Updated Feb 3, 2025Feb 3, 2025

• flamingo-tools

  Public
  lightsheet-moser

  Python

  •1•2•7•0•Updated Feb 2, 2025Feb 2, 2025

• medico-sam

  Public
  Segment Anything for Medical Imaging

  sammedical-imagingsemantic-segmentation+ 2interactive-segmentationsegment-anything

  Python

  •

  MIT License

  •0•8•0•0•Updated Feb 2, 2025Feb 2, 2025

• peft-sam

  Public
  Parameter Efficient Fine-Tuning of Segment Anything Model

  sammedical-imagingsegmentation+ 7microscopypeftfinetuningsegment-anythingqloramicro-sammedico-sam

  Python

  •

  MIT License

  •0•1•2•1•Updated Feb 2, 2025Feb 2, 2025

• micro-sam

  Public
  Segment Anything for Microscopy

  segmentationcell-segmentationmicroscopy-images+ 4nuclei-segmentationnaparisegment-anythingmitochondria-segmentation

  Jupyter Notebook

  •

  MIT License

  •48•386•50•17•Updated Jan 29, 2025Jan 29, 2025

• .github

  Public
  0•0•0•0•Updated Jan 5, 2025Jan 5, 2025

• vimunet-benchmarking

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

  Python

  •1•0•1•0•Updated Jan 3, 2025Jan 3, 2025

• micro_sam-feedstock

  Public
  A conda-smithy repository for micro_sam.

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

  •5•0•0•0•Updated Dec 21, 2024Dec 21, 2024

• protein-detection

  Public
  0•0•0•0•Updated Dec 13, 2024Dec 13, 2024

• pdo_genetic_analysis

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Nov 25, 2024Nov 25, 2024

• user-study-v3

  Public
  Python

  •0•1•0•0•Updated Nov 14, 2024Nov 14, 2024

• Probabilistic-Domain-Adaptation

  Public
  Probabilistic Domain Adaptation for Biomedical Image Segmentation

  electron-microscopydomain-adaptationpseudo-label+ 5lung-xrayprobabilistic-unetlivecelldeep-learningsegmentation

  Python

  •

  MIT License

  •0•6•0•0•Updated Aug 19, 2024Aug 19, 2024

• oc-sync

  Public
  Sync ownCloud

  Python

  •

  MIT License

  •0•0•0•0•Updated Mar 20, 2024Mar 20, 2024

• dl-for-micro

  Public
  Course and exercises on deep learning for microscopy image analysis

  Jupyter Notebook

  •

  MIT License

  •0•13•3•0•Updated Mar 6, 2024Mar 6, 2024

• pyseg_system

  Public
  De novo analysis for cryo-electron tomography

  C

  •

  Other

  •4•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

  •

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

  •5.1k•0•0•0•Updated Oct 4, 2023Oct 4, 2023

• samapi

  Public
  Segment Anything Model API

  Python

  •

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

  •14•0•0•0•Updated Sep 4, 2023Sep 4, 2023

• qupath-extension-sam

  Public
  QuPath extension for Segment Anything Model (SAM)

  Java

  •

  GNU General Public License v3.0

  •15•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