Top 11 microscopy Open-Source Projects

relion

1 423 6.2 C++

Image-processing software for cryo-electron microscopy
pathml

2 358 6.9 Python

Tools for computational pathology

Project mention: Hilo Semanal de Consultas IT - Asesoría Técnica, Desarrollo Profesional y Aprendizaje | /r/chileIT | 2023-06-28

InfluxDB

www.influxdata.com sponsored

Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.
cucim

1 306 8.6 Jupyter Notebook

cuCIM - RAPIDS GPU-accelerated image processing library

Project mention: FLaNK Stack Weekly for 13 November 2023 | dev.to | 2023-11-13

aicsimageio

1 192 6.8 Python

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

1 118 6.1 Jupyter Notebook

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

1 51 8.8 Shell

Open and Affordable Quantitative Imaging Platform

Project mention: PlanktoScope: Open and Affordable Quantitative Imaging Platform | news.ycombinator.com | 2023-10-07

focus_annotator

6 25 2.9 Rust

This is a tool to annotate the focus plane of z-stacked images.
WorkOS

workos.com sponsored

The modern identity platform for B2B SaaS. The APIs are flexible and easy-to-use, supporting authentication, user identity, and complex enterprise features like SSO and SCIM provisioning.
BioImager

1 11 8.1 C#

A .NET microscopy imaging application based on Bio library. Supports various microscopes by using imported libraries & GUI automation. Supports XInput game controllers to move stage, take images, run ImageJ macros on images or Bio C# scripts.

Project mention: Anyone developing .NET microscopy applications or libraries? | /r/microscopy | 2023-05-03

I'm a C# developer creating .NET microscopy applications & libraries. I'm looking for other programmers who are working on similar projects to collaborate and create a C# micro-manager like program https://github.com/BiologyTools/BioImager. I've tried looking for other projects on Github but all are written in java or python.

BioGTK

1 8 9.1 C#

A cross platform version of Bio library & program. Bio is a library & program for annotating, & editing various microscopy imaging formats using Bioformats supported images. including whole slide, pyramidal & series.

Project mention: I made a .NET6 library & program which integrates with ImageJ. | /r/ImageJ | 2023-08-04

https://github.com/BiologyTools/BioGTK A cross platform version of Bio library & program. Bio is a library & program for annotating, & editing various microscopy imaging formats using Bioformats supported images. including whole slide, pyramidal & series.

Bio

3 4 0.0 C#

A .NET library & program for annotating, & editing various microscopy imaging formats using Bioformats supported images. including whole slide, pyramidal & series. (by BiologyTools)
pyCellID

2 1 0.0 Python

Functions to analyze Cell-ID single-cell cytometry data using python language.

NOTE: The open source projects on this list are ordered by number of github stars. The number of mentions indicates repo mentiontions in the last 12 Months or since we started tracking (Dec 2020).