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Microscopy GitHub Repositories (2026) · Open Source Tools

Discover the best Microscopy open source repositories on GitHub. Explore trending tools, live star counts, source code, and developer projects updated daily.

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6 matching projects · updated Nov 13, 2026 How we rank ↗

#1 TRENDING deepinv/deepinv Python 2023

DeepInverse: a PyTorch library for solving imaging inverse problems using deep learning

◇ computational-imaging ◇ deblurring ◇ deep-learning ◇ denoising

226 ↑ +8 today

#2 TRENDING aafkegros/MicroscopyNodes Python 2023

Loading and handling microscopy data in blender

◇ blender ◇ blender-addon ◇ microscopy ◇ volume-rendering

13 ↑ +1 today

#3 TRENDING PytorchConnectomics/pytorch_connectomics Python 2019

PyTorch Connectomics: segmentation toolbox for EM connectomics

◇ biomedical-image-processing ◇ computer-vision ◇ connectomics ◇ deep-learning

89 ↑ +1 today

#4 TRENDING scalableminds/webknossos TypeScript 2012

Visualize, share and annotate your large 3D images online

◇ connectomics ◇ em ◇ hacktoberfest ◇ microscopy

42 ↑ +1 today

#5 TRENDING seung-lab/cloud-volume Python 2017

Read and write Neuroglancer datasets programmatically.

◇ big-data ◇ biomedical-image-processing ◇ chunked-image ◇ cloud

54 ↑ +1 today

#6 TRENDING okunator/cellseg_models.pytorch Python 2022

Encoder-Decoder Cell and Nuclei segmentation models

◇ ai ◇ cell-segmentation ◇ cellpose ◇ digital-pathology

5 ↑ +1 today

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