Inviwo is a software framework for rapid visualization prototyping. It is freely available under the Simplified BSD License and runs on Windows, Linux, and Mac OS X. The framework is easily extendable through external modules and projects. The core is written in C/C++ with minor dependencies. It supports modern
The OpenFlexure Microscope is a 3D printable microscope, including a precise mechanical stage to move the sample and focus the optics. There are many different options for the optics, ranging from a webcam lens to a 100x, oil immersion objective. It comes with a sophisticated guide that helps anyone print
MicroscoPy is an open-source MICROSCOPE built using LEGO bricks, 3D-printing, Arduino and Raspberry Pi. The project is started by Yuksel Temiz, an engineer and a designer from Switzerland, who later released it as an open-source for educational purposes. It is released and hosted by IBM, with full instructions, video tutorials
I planned to write about this amazing project months ago, soon after I wrote about OpenSeadragon library. I recommended the project already to my colleagues who are teaching at medical schools. Some of my relatives who are studying medicine. The Human Protein Atlas is a Swedish-based project that started 2003
What's MicroDraw? MicroDraw is a lightweight web-based collaborative annotation application for displaying and viewing large-scale (DeepZoom) images. It's completely free and open-source software that comes with no restrictions to use or to modify. It's a self-hosted application which means it can be installed and hosted at private hosting for teams.
While consulting for medical projects over the years and working on some, I collected hundreds of domain-specific libraries and frameworks built to help developers make medical applications. However, many of the libraries were not supported or popular enough to survive as they were abandoned by their creators over the years.
What is Whole-slide image or Virtual Slides? Whole-slide images (Virtual Slides), are a high-resolution image of physical histopathology scanned with special scanners, that produces the images in gigapixels. It allows scientists, researchers, clinical pathologists to use software to zoom for regions of interest ROIs. Whole-slide images viewers are used in
OME (Open Microscopy Environment) is an open-source initiative aiming to produce open-source software and format standards for microscopy data. The project is started by researchers from the University of Dundee, later it gathered the attention and support from researchers, developers, & scientists from all over the world, from universities, institutes, laboratories,
OpenSlide is a C library for processing, reading whole-slide images (virtual slides). It's the engine behind many digital pathology projects open source and closed source. It provides a simple performance-focused interface for parsing and processing virtual slides images format (WSI). OpenSlide has Python, Java, and Julia language bindings. Developers who
BioImageXD is an open-source microscopy imaging software for processing, analyzing, visualizing, and rendering multi-dimensional microscopy images. The project was carried out by a team of researchers including microscopists, cell biologists and software engineers from the Universities of Jyväskylä and Turku in Finland, Max Planck Institute CBG in Dresden, Germany and
Cytomine is a web-based open source solution, aiming to empower whole-slide image processing, & analysis with machine learning algorithms. It's built to ease collaboration among researchers. Cytomine is built by a group of researchers from Montefiore Institute (University of Liège, Belgium) who are developing machine learning algorithms and big data software
Orbit is an open source software package built to empower whole slide images (Virtual slides) processing/analysis with powerful AI models for researchers and pathologists. Orbit is an advanced whole-slide image viewer with advanced image analysis algorithms, built-in machine learning models for tissue quantification, script editor to write, edit models
QuPath is a free & open source quantitative Pathology & Bioimage Analysis software. Because QuPath is built with Java it is cross-platform, it's available for download for Windows, Mac OSX and Linux. It is built to provide whole slide image analysis required in clinical pathology. QuPath is developed at Division of Pathology