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

OME (Open Microscopy Environment) develops open-source software and data format standards for the storage and manipulation of biological light microscopy data. A joint project between universities, research establishments and industry in Europe and the USA, OME has over 20 active researchers with... Read more

Pipeline for particle picking in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Also featuring micrograph and tomogram denoising with DNNs.

Usiigaci: stain-free cell tracking in phase contrast microscopy enabled by supervised machine learning

A Python GUI-based framework for segmentation, tracking and cell cycle annotations of microscopy data

PyTorch Connectomics: segmentation toolbox for EM connectomics

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

A Python interface to access neuroanatomical atlases

Non-comprehensive list of projects and resources related to open microscopy.

Visualize, share and annotate your large 3D images online