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    45 repositories

    • torch-mesmer

      Public
      pytorch implementation of mesmer
      Python
      •
      Apache License 2.0
      •1•1•9•0•Updated Aug 13, 2026Aug 13, 2026

    • torch-spots

      Public
      PyTorch implementation of SpotNet and its decoding in PyTorch
      Python
      •0•0•0•0•Updated Aug 13, 2026Aug 13, 2026

    • torch-tracking

      Public
      PyTorch implementation of Caliban
      Python
      •1•0•0•0•Updated Aug 13, 2026Aug 13, 2026

    • deepcell-types

      Public
      Python
      •
      Apache License 2.0
      •4•10•7•0•Updated Aug 11, 2026Aug 11, 2026

    • ftu_dev

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Aug 6, 2026Aug 6, 2026

    • deepcell-auth

      Public
      Authentication client for deepcell ecosystem
      Python
      •
      Apache License 2.0
      •2•0•0•0•Updated Aug 5, 2026Aug 5, 2026

    • DeepCellTypes-2026_Wang_et_al

      Public
      Jupyter Notebook
      •
      Other
      •1•0•0•0•Updated Jul 13, 2026Jul 13, 2026

    • torch-dynamicnuclearnet

      Public
      DynamicNuclearNet implemented in PyTorch
      Python
      •0•0•0•1•Updated Jun 29, 2026Jun 29, 2026

    • deepcell-spots

      Public
      Deep Learning Library for Spot Detection
      deep-learningtensorflowbiological-data-analysis
      deep-learningtensorflowbiological-data-analysisspot-detection
      Python
      •
      Apache License 2.0
      •5•24•5•0•Updated Jun 4, 2026Jun 4, 2026

    • deepcell-tracking

      Public
      Track cells and build cell lineages
      Python
      •
      Apache License 2.0
      •6•35•9•0•Updated Jun 4, 2026Jun 4, 2026

    • deepcell-label

      Public
      Cloud-based data annotation tools for biological images
      reactjavascriptpython
      reactjavascriptpythonflaskbiologyimage-segmentationannotate-imagesxstate
      JavaScript
      •
      Apache License 2.0
      •17•85•61•8•Updated Jun 4, 2026Jun 4, 2026

    • cellSAM

      Public
      Codebase for "A Foundation Model for Cell Segmentation"
      Python
      •
      Apache License 2.0
      •37•210•41•8•Updated Jun 4, 2026Jun 4, 2026

    • deepcell-tf

      Public
      Deep Learning Library for Single Cell Analysis
      deep-learningtensorflowinstance-segmentation
      deep-learningtensorflowinstance-segmentationcell-biology
      Python
      •
      Apache License 2.0
      •108•477•54•2•Updated Jun 4, 2026Jun 4, 2026

    • cryosearch

      Public
      Cryo electron tomography docking
      Python
      •0•0•0•0•Updated May 16, 2026May 16, 2026

    • cellsam-demo-site

      Public
      Source code for cellsam.deepcell.org
      TypeScript
      •1•0•2•20•Updated Feb 14, 2026Feb 14, 2026

    • deepcell-label-utils

      Public
      Utilities for spatial cell labels
      Python
      •
      Other
      •0•0•0•1•Updated Dec 22, 2025Dec 22, 2025

    • sfk_dms_paper

      Public
      Changhua Yu's code for SFK DMS paper
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Nov 8, 2025Nov 8, 2025

    • intro-to-deepcell

      Public archive
      An introduction to deepcell and deep learning
      Jupyter Notebook
      •
      Other
      •27•155•8•0•Updated Oct 21, 2024Oct 21, 2024

    • Caliban-2024_Schwartz_et_al

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •0•5•0•0•Updated Aug 8, 2024Aug 8, 2024

    • Polaris-2023_Laubscher_et_al

      Public
      Jupyter Notebook
      •
      Other
      •1•0•0•0•Updated Jan 31, 2024Jan 31, 2024

    • hubmap-mean-expression-example

      Public
      Minimal analysis example of data from cytokit+sprm pipeline output
      Python
      •0•0•0•0•Updated Dec 19, 2023Dec 19, 2023

    • deepcell-toolbox

      Public
      Data processing tools associated with deepcell
      Python
      •
      Other
      •9•11•7•0•Updated Nov 7, 2023Nov 7, 2023

    • deepcelltypes-demo-08-2023

      Public
      Executable demo of deepcelltypes model pipeline
      Python
      •0•0•0•0•Updated Aug 26, 2023Aug 26, 2023

    • kiosk-imageJ-plugin

      Public
      An ImageJ Plugin for interacting with the DeepCell Kiosk
      Java
      •
      Other
      •2•4•9•2•Updated Aug 24, 2023Aug 24, 2023

    • kiosk-console

      Public
      DeepCell Kiosk Distribution for Kubernetes on GKE and AWS
      kuberneteshelmtensorflow-serving
      kuberneteshelmtensorflow-servinghelmfile
      Shell
      •
      Other
      •7•37•15•0•Updated Jul 12, 2023Jul 12, 2023

    • kiosk-redis-consumer

      Public
      Consume the Kiosk's Redis Events
      Python
      •
      Other
      •0•0•6•1•Updated Jul 12, 2023Jul 12, 2023

    • deepcell-label-processing

      Public
      Scripts for processing and converting raw data to label format and creating DCL projects
      Python
      •1•1•0•1•Updated Jul 7, 2023Jul 7, 2023

    • kiosk-data-processing

      Public
      DEPRECATED: gRPC API for pre- and post-processing data
      Python
      •0•0•0•2•Updated Jul 5, 2023Jul 5, 2023

    • deepcell-datasets

      Public
      React App for hosting curated datasets.
      reactserverless
      reactserverless
      Python
      •
      Other
      •0•0•11•7•Updated Jun 26, 2023Jun 26, 2023

    • bebi205

      Public
      Repo for Caltech's Be/Bi 205 course
      Jupyter Notebook
      •
      Other
      •0•0•0•0•Updated May 31, 2023May 31, 2023
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