Repositories list

• eps-Seg

  Public
  A hierarchical variational autoencoder based method for semantic segmentation of Electron Microscopy data.

  Jupyter Notebook

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

  •00 forks in juglab/eps-Seg•66 stars in juglab/eps-Seg•33 issues in juglab/eps-Seg•00 pull requests in juglab/eps-Seg•Updated Oct 23, 2026Oct 23, 2026

• CiliaAI-minicourse

  Public
  Hands-on exercises for the Cilia-AI / CiliaConnect mini-course on image analysis and AI (denoising with BM3D and Noise2Void)

  Jupyter Notebook

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  Creative Commons Attribution 4.0 International

  •00 forks in juglab/CiliaAI-minicourse•00 stars in juglab/CiliaAI-minicourse•00 issues in juglab/CiliaAI-minicourse•00 pull requests in juglab/CiliaAI-minicourse•Updated Oct 7, 2026Oct 7, 2026

• napari-n2v

  Public
  A self-supervised denoising algorithm.

  Python

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

  •55 forks in juglab/napari-n2v•3131 stars in juglab/napari-n2v•1313 issues in juglab/napari-n2v•00 pull requests in juglab/napari-n2v•Updated Oct 5, 2026Oct 5, 2026

• MicroSSIM

  Public
  Range Invariant SSIM

  Jupyter Notebook

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

  •00 forks in juglab/MicroSSIM•33 stars in juglab/MicroSSIM•11 issue in juglab/MicroSSIM•00 pull requests in juglab/MicroSSIM•Updated Oct 5, 2026Oct 5, 2026

• lambdaSplit

  Public
  Self-Supervised Content-Aware Spectral Unmixing for Fluorescence Microscopy

  00 forks in juglab/lambdaSplit•00 stars in juglab/lambdaSplit•00 issues in juglab/lambdaSplit•00 pull requests in juglab/lambdaSplit•Updated Sep 7, 2026Sep 7, 2026

• SWITi_reproducibility

  Public
  Experiments for "SWITi: Quantifying and Reducing Tiling Artifacts with Sliding Window Inner Tiling" (https://arxiv.org/abs/2607.18990)

  Python

  •

  MIT License

  •00 forks in juglab/SWITi_reproducibility•00 stars in juglab/SWITi_reproducibility•00 issues in juglab/SWITi_reproducibility•00 pull requests in juglab/SWITi_reproducibility•Updated Sep 3, 2026Sep 3, 2026

• eps-SegFormer

  Public
  Transformer-based implementation of eps-Seg

  Python

  •00 forks in juglab/eps-SegFormer•11 star in juglab/eps-SegFormer•00 issues in juglab/eps-SegFormer•00 pull requests in juglab/eps-SegFormer•Updated Sep 1, 2026Sep 1, 2026

• resmatching

  Public
  Python

  •

  MIT License

  •11 fork in juglab/resmatching•00 stars in juglab/resmatching•00 issues in juglab/resmatching•00 pull requests in juglab/resmatching•Updated Aug 19, 2026Aug 19, 2026

• HazeMatching

  Public
  Code for our CVPR 2026 (Findings) paper https://arxiv.org/abs/2506.22397.

  Python

  •

  MIT License

  •22 forks in juglab/HazeMatching•66 stars in juglab/HazeMatching•00 issues in juglab/HazeMatching•00 pull requests in juglab/HazeMatching•Updated Aug 8, 2026Aug 8, 2026

• TilArtMetrics

  Public
  Metrics for detection and quantification of tiling artifacts as described in "F. Carrara et al., SWITi: Quantifying and Reducing Tiling Artifacts with Sliding W…

  Python

  •

  MIT License

  •00 forks in juglab/TilArtMetrics•22 stars in juglab/TilArtMetrics•00 issues in juglab/TilArtMetrics•00 pull requests in juglab/TilArtMetrics•Updated Jul 27, 2026Jul 27, 2026

• MicroSplit

  Public
  Experiments for MicroSplit were done using this code.

  Jupyter Notebook

  •33 forks in juglab/MicroSplit•11 star in juglab/MicroSplit•00 issues in juglab/MicroSplit•00 pull requests in juglab/MicroSplit•Updated May 19, 2026May 19, 2026

• PyTr2d

  Public
  Python based Tracking in 2D

  Python

  •

  BSD 2-Clause "Simplified" License

  •00 forks in juglab/PyTr2d•11 star in juglab/PyTr2d•00 issues in juglab/PyTr2d•00 pull requests in juglab/PyTr2d•Updated Apr 13, 2026Apr 13, 2026

• CellPaintMONO

  Public
  tools for analysis and comparison of cell painting data

  Python

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

  •00 forks in juglab/CellPaintMONO•00 stars in juglab/CellPaintMONO•00 issues in juglab/CellPaintMONO•00 pull requests in juglab/CellPaintMONO•Updated Jan 12, 2026Jan 12, 2026

• scSplit

  Public
  scSplit: Bringing Severity Cognizance to Image Decomposition in Fluorescence Microscopy

  Jupyter Notebook

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  Apache License 2.0

  •481481 forks in juglab/scSplit•00 stars in juglab/scSplit•00 issues in juglab/scSplit•00 pull requests in juglab/scSplit•Updated Dec 4, 2025Dec 4, 2025

• denoiSplit

  Public
  Jupyter Notebook

  •

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

  •11 fork in juglab/denoiSplit•33 stars in juglab/denoiSplit•00 issues in juglab/denoiSplit•00 pull requests in juglab/denoiSplit•Updated Nov 27, 2025Nov 27, 2025

• featureforest

  Public
  A napari plugin for making image annotation using feature space of vision transformers and Random Forest classifier

  Python

  •

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

  •22 forks in juglab/featureforest•2424 stars in juglab/featureforest•33 issues in juglab/featureforest•00 pull requests in juglab/featureforest•Updated Nov 24, 2025Nov 24, 2025

• HDN

  Public
  This repository hosts the code for HDN (associated with the paper https://arxiv.org/pdf/2104.01374.pdf) for pixel and structured noise removal for microscopy an…

  Python

  •

  Other

  •88 forks in juglab/HDN•3434 stars in juglab/HDN•44 issues in juglab/HDN•11 pull request in juglab/HDN•Updated Nov 7, 2025Nov 7, 2025

• MycroVerse

  Public
  Cell Simulator to map parametrical distributions into various modalities

  Jupyter Notebook

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  GNU General Public License v3.0

  •00 forks in juglab/MycroVerse•22 stars in juglab/MycroVerse•00 issues in juglab/MycroVerse•11 pull request in juglab/MycroVerse•Updated Oct 13, 2025Oct 13, 2025

• Tiling-Artefact-Quantification

  Public
  Tools to quantify and compare tiling artifacts in model predictions. Our framework measures and visualizes these differences, making it easier to compare artifa…

  Jupyter Notebook

  •00 forks in juglab/Tiling-Artefact-Quantification•00 stars in juglab/Tiling-Artefact-Quantification•00 issues in juglab/Tiling-Artefact-Quantification•00 pull requests in juglab/Tiling-Artefact-Quantification•Updated Aug 20, 2025Aug 20, 2025

• uSplit

  Public
  Python

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  MIT License

  •55 forks in juglab/uSplit•77 stars in juglab/uSplit•22 issues in juglab/uSplit•00 pull requests in juglab/uSplit•Updated Jun 16, 2025Jun 16, 2025

• DivNoising

  Public
  DivNoising is an unsupervised denoising method to generate diverse denoised samples for any noisy input image. This repository contains the code to reproduce th…

  unsupervised-denoisingnoise-modeldiverse-denoising+ 1

  unsupervised-denoisingnoise-modeldiverse-denoisingfully-convolutional-vae

  Python

  •

  Other

  •77 forks in juglab/DivNoising•4646 stars in juglab/DivNoising•00 issues in juglab/DivNoising•00 pull requests in juglab/DivNoising•Updated Apr 16, 2025Apr 16, 2025

• cellpose-bmz-wrapper

  Public
  A wrapper to pack cellpose model for bioimage model zoo

  Python

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

  •00 forks in juglab/cellpose-bmz-wrapper•00 stars in juglab/cellpose-bmz-wrapper•00 issues in juglab/cellpose-bmz-wrapper•00 pull requests in juglab/cellpose-bmz-wrapper•Updated Apr 9, 2025Apr 9, 2025

• n2v

  Public
  This is the implementation of Noise2Void training.

  Python

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  Other

  •119119 forks in juglab/n2v•496496 stars in juglab/n2v•2424 issues in juglab/n2v•33 pull requests in juglab/n2v•Updated Dec 18, 2024Dec 18, 2024

• labkit-ui

  Public
  Advanced Tool for Labeling And Segmentation

  Java

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  BSD 2-Clause "Simplified" License

  •2323 forks in juglab/labkit-ui•4141 stars in juglab/labkit-ui•6464 issues in juglab/labkit-ui•44 pull requests in juglab/labkit-ui•Updated Oct 21, 2024Oct 21, 2024

• labkit-pixel-classification

  Public
  Java

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  BSD 2-Clause "Simplified" License

  •66 forks in juglab/labkit-pixel-classification•66 stars in juglab/labkit-pixel-classification•33 issues in juglab/labkit-pixel-classification•00 pull requests in juglab/labkit-pixel-classification•Updated Aug 29, 2024Aug 29, 2024

• bioimageio-uploader

  Public
  Svelte

  •22 forks in juglab/bioimageio-uploader•00 stars in juglab/bioimageio-uploader•00 issues in juglab/bioimageio-uploader•00 pull requests in juglab/bioimageio-uploader•Updated Aug 28, 2024Aug 28, 2024

• AI4LifeSubmissions

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks in juglab/AI4LifeSubmissions•11 star in juglab/AI4LifeSubmissions•00 issues in juglab/AI4LifeSubmissions•00 pull requests in juglab/AI4LifeSubmissions•Updated Jul 30, 2024Jul 30, 2024

• git_playground

  Public
  00 forks in juglab/git_playground•00 stars in juglab/git_playground•00 issues in juglab/git_playground•00 pull requests in juglab/git_playground•Updated Jun 19, 2024Jun 19, 2024

• cryoCARE_pip

  Public
  PIP package of cryoCARE

  Python

  •

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

  •1919 forks in juglab/cryoCARE_pip•4646 stars in juglab/cryoCARE_pip•2121 issues in juglab/cryoCARE_pip•22 pull requests in juglab/cryoCARE_pip•Updated Apr 2, 2024Apr 2, 2024

• core-bioimage-io-python

  Public
  Python libraries for loading, running and packaging bioimage.io models

  Jupyter Notebook

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  MIT License

  •2323 forks in juglab/core-bioimage-io-python•00 stars in juglab/core-bioimage-io-python•00 issues in juglab/core-bioimage-io-python•00 pull requests in juglab/core-bioimage-io-python•Updated Mar 24, 2024Mar 24, 2024