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3dem /relion

Image-processing software for cryo-electron microscopy

gui hpc molecular-structures cuda image-processing nvidia high-performance-computing graphics-programming ctf regularization cryo-em microscopy likelihood maximum-likelihood optimization-algorithms relion molecular-biology atomistic-models biomolecular-dynamics microscope

UpdatedJan 14, 2026
C++

BMIRDS /deepslide

Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for classification of high resolution whole-slide images, often microscopy or histopathology images.

cancer resnet microscopy sliding-windows lung wsi medical-image-analysis pathology-image histopathology-images

UpdatedJun 7, 2024
Python

rapidsai /cucim

cuCIM - RAPIDS GPU-accelerated image processing library

computer-vision gpu cuda image-processing nvidia medical-imaging segmentation image-analysis microscopy digital-pathology image-data multidimensional-image-processing

UpdatedFeb 20, 2026
Jupyter Notebook

pathml

Dana-Farber-AIOS /pathml

Tools for computational pathology

python machine-learning research deep-learning pytorch image-analysis microscopy biomedical-image-processing fluorescence-microscopy-imaging digital-pathology pathology computational-pathology spatial-transcriptomics histopathology pathml

UpdatedOct 24, 2025
Python

CellViT

TIO-IKIM /CellViT

CellViT: Vision Transformers for Precise Cell Segmentation and Classification

python ai ml pytorch cell microscopy digitalpathology

UpdatedJul 23, 2025
Python

pycroscopy /pycroscopy

Scientific analysis of nanoscale materials imaging data

visualization atom machine-learning statistics afm signal-processing stm fft electron-microscopy stem materials-science scanning microscopy imaging spectroscopy infrared raman atomic-force-microscopy scanning-probe-microscopy scanning-tunnelling-microscopy

UpdatedSep 12, 2025
Jupyter Notebook

pyclesperanto_prototype

clEsperanto /pyclesperanto_prototype

GPU-accelerated bio-image analysis focusing on 3D+t microscopy image data

gpu-acceleration microscopy bioimage-analysis

UpdatedFeb 21, 2025
Jupyter Notebook

DeepTrack2

DeepTrackAI /DeepTrack2

DeepTrack2 is a modular Python library for generating, manipulating, and analyzing image data pipelines for machine learning and experimental imaging.

machine-learning deep-learning image-processing optics microscopy data-augmentation biophysics soft-matter computational-pipelines photonics superresolution

UpdatedFeb 19, 2026
Jupyter Notebook

cellfinder

brainglobe /cellfinder

Automated 3D cell detection in very large images

python deep-learning neuroscience image-analysis microscopy imaging neuroanatomy cell-detection

UpdatedFeb 3, 2026
Python

AllenCellModeling /aicsimageio

Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python

python xarray scientific-computing imageio bio-formats dask image-metadata microscopy scientific-formats

UpdatedDec 1, 2025
Python

atomai

pycroscopy /atomai

Deep and Machine Learning for Microscopy

machine-learning deep-learning materials jupyter-notebook pytorch ensemble-learning electron-microscopy materials-science microscopy imaging semantic-segmentation fully-convolutional-networks multivariate-analysis variational-autoencoders deep-kernel-learning scanning-probe-microscopy google-colaboratory

UpdatedJun 24, 2025
Python

PytorchConnectomics /pytorch_connectomics

PyTorch Connectomics: segmentation toolbox for EM connectomics

computer-vision deep-learning neuroscience pytorch segmentation connectomics microscopy biomedical-image-processing

UpdatedFeb 20, 2026
Python

awesome-biological-image-analysis

hallvaaw /awesome-biological-image-analysis

A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.

awesome imagej biology image-processing cellprofiler awesome-list segmentation image-analysis microscopy imaging bioimage-analysis

UpdatedJan 27, 2026

brainglobe /brainglobe-atlasapi

A Python interface to access neuroanatomical atlases

python visualisation neuroscience registration microscopy brain atlases

UpdatedFeb 20, 2026
Python

seung-lab /cloud-volume

Read and write Neuroglancer datasets programmatically.

python cloud big-data serverless numpy matrix s3 gcs mesh tensor electron-microscopy connectomics microscopy skeletons biomedical-image-processing volumetric-data microscopy-images neuroglancer large-image chunked-image

UpdatedFeb 13, 2026
Python

webknossos

scalableminds /webknossos

Visualize, share and annotate your large 3D images online

neurobiology reconstruction connectomics em microscopy hacktoberfest microscopy-images

UpdatedFeb 20, 2026
TypeScript

zeiss-microscopy /OAD

Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools and AI tools.

python open-source workflow machine-learning automation scripting python-script image-processing zen acquisition image-analysis microscopy imaging zen-blue oad

UpdatedFeb 19, 2026
Jupyter Notebook

aafkegros /MicroscopyNodes

Loading and handling microscopy data in blender

blender volume-rendering microscopy blender-addon

UpdatedNov 8, 2025
Python

brainglobe /brainreg

Automated 3D brain registration with support for multiple species and atlases.

neuroscience registration microscopy brain neuroanatomy atlases

UpdatedFeb 13, 2026
Python

jungmannlab /picasso

A collection of tools for painting super-resolution images

microscopy super-resolution dna-paint smlm

UpdatedFeb 16, 2026
Python

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