delmic/odemis

Microscope control and image acquisition integrated with ImageJ

Python machine vision platform

Nion Swift is open source scientific image processing software integrating hardware control, data acquisition, visualization, processing, and analysis using Python. Nion Swift is easily extended using Python. It runs on Windows, Linux, and macOS.

The python-microscopy environment - an open-source package for light microscopy

Python library for control of microscope devices, supporting hardware triggers and distribution of devices over the network for performance and flexibility.

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 strong links to the microscopy community. Funded by private and public research grants, OME has been a major force on the international microscopy stage since 2000.

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

Microscopy workflow tool for TIFF datasets, ROI extraction, and AI-based analysis, developed with JAMSTEC and the authors of Nishimura et al. (Scientific Reports, 2025).

Pure python/C++ micro-manager ecosystem