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    95 repositories

    • eps-Seg

      Public
      A hierarchical variational autoencoder based method for semantic segmentation of Electron Microscopy data.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•0•Updated Feb 11, 2026Feb 11, 2026

    • MicroSSIM

      Public
      Range Invariant SSIM
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•1•1•Updated Feb 4, 2026Feb 4, 2026

    • CellPaintMONO

      Public
      tools for analysis and comparison of cell painting data
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jan 12, 2026Jan 12, 2026

    • MicroSplit

      Public
      Experiments for MicroSplit were done using this code.
      Jupyter Notebook
      •2•0•0•0•Updated Dec 19, 2025Dec 19, 2025

    • scSplit

      Public
      scSplit: Bringing Severity Cognizance to Image Decomposition in Fluorescence Microscopy
      Jupyter Notebook
      •
      Apache License 2.0
      •482•0•0•0•Updated Dec 4, 2025Dec 4, 2025

    • denoiSplit

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•0•0•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
      •2•21•3•0•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
      •8•35•4•1•Updated Nov 7, 2025Nov 7, 2025

    • MycroVerse

      Public
      Cell Simulator to map parametrical distributions into various modalities
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•2•0•1•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
      •0•0•0•0•Updated Aug 20, 2025Aug 20, 2025

    • uSplit

      Public
      Python
      •
      MIT License
      •5•7•2•0•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-denoisingfully-convolutional-vae
      Python
      •
      Other
      •7•44•0•0•Updated Apr 16, 2025Apr 16, 2025

    • cellpose-bmz-wrapper

      Public
      A wrapper to pack cellpose model for bioimage model zoo
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 9, 2025Apr 9, 2025

    • n2v

      Public
      This is the implementation of Noise2Void training.
      Python
      •
      Other
      •118•476•24•3•Updated Dec 18, 2024Dec 18, 2024

    • labkit-ui

      Public
      Advanced Tool for Labeling And Segmentation
      Java
      •
      BSD 2-Clause "Simplified" License
      •22•40•62•3•Updated Oct 21, 2024Oct 21, 2024

    • labkit-pixel-classification

      Public
      Java
      •
      BSD 2-Clause "Simplified" License
      •6•6•2•0•Updated Aug 29, 2024Aug 29, 2024

    • bioimageio-uploader

      Public
      Svelte
      •2•0•0•0•Updated Aug 28, 2024Aug 28, 2024

    • AI4LifeSubmissions

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Jul 30, 2024Jul 30, 2024

    • git_playground

      Public
      0•0•0•0•Updated Jun 19, 2024Jun 19, 2024

    • napari-n2v

      Public
      A self-supervised denoising algorithm.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•28•13•0•Updated Apr 6, 2024Apr 6, 2024

    • cryoCARE_pip

      Public
      PIP package of cryoCARE
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •16•45•20•1•Updated Apr 2, 2024Apr 2, 2024

    • core-bioimage-io-python

      Public
      Python libraries for loading, running and packaging bioimage.io models
      Jupyter Notebook
      •
      MIT License
      •22•0•0•0•Updated Mar 24, 2024Mar 24, 2024

    • EmbedSeg

      Public
      Code Implementation for EmbedSeg, an Instance Segmentation Method for Microscopy Images
      deep-learninginstance-segmentationtest-time-augmentationspatial-embeddings
      Python
      •
      Other
      •24•127•10•0•Updated Feb 14, 2024Feb 14, 2024

    • core-bioimage-io-widgets

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•2•Updated Dec 11, 2023Dec 11, 2023

    • solvathon_sorting

      Public
      Sorting project(10)
      Jupyter Notebook
      •0•0•0•0•Updated Oct 12, 2023Oct 12, 2023

    • MAESTER

      Public
      Masked Autoencoder Guided Segmentation at Pixel Resolution
      Python
      •
      MIT License
      •6•0•0•0•Updated Oct 3, 2023Oct 3, 2023

    • labkit-command-line

      Public
      Labkit Command Line - Segment huge images on a cluster
      Java
      •
      BSD 2-Clause "Simplified" License
      •3•3•6•1•Updated Sep 25, 2023Sep 25, 2023

    • DenoiSeg

      Public
      Joint training of denoising and segmentation.
      Jupyter Notebook
      •
      Other
      •21•76•6•0•Updated Aug 29, 2023Aug 29, 2023

    • pn2v

      Public
      This is our implementation of Probabilistic Noise2Void
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •12•77•1•0•Updated Aug 28, 2023Aug 28, 2023

    • PPN2V

      Public
      Code Implementation for the publication "Fully Unsupervised Probabilistic Noise2Void"
      unsupervised-denoisingnoise-model
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •10•57•2•0•Updated Aug 28, 2023Aug 28, 2023