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 at the University of Edinburgh. The project received funds from Invest Northern Ireland, and Cancer Research UK Accelerator.
QuPath Screenshot
Highlights
Cross-platform: Windows, Linux, Mac OSX
Lightweight
Powerful visualization kit
Provides fast analysis
Rich annotation tools
Workflows for both IHC and H&E analysis
Novel algorithms for common tasks, e.g. cell segmentation, Tissue microarray dearraying
Machine learning powered analysis
Clear data model
Easy to integrate with Matlab and ImageJ
Multiple formats for export
Automated tasks support
Automated Analysis
Powerful Scripting tool
Supports data exchange with other open-source tools like ImageJ
QuPath Screenshot
Features
Whole-slide viewer
Dynamic color transformation
Support compressed and uncompressed files
Biomarker quantification
Tissue Microarray support
Sophisticated tumor identification
Mini-viewer
Multiple display options
Flexible object classification
Interactive tools to display, zoom, scale, navigate
Image exports
User-friendly automated analysis
Stain estimation
Analytics
Reporting
License
QuPath is released under GNU General Public License v3.0
Platforms
QuPath is a cross-platform it works for Windows, Linux, & Mac OSX
Download
The current stable version v0.1.2 (3 July/ 2019), is available for download, There is an early release of QuPath v0.2.0 is available for testing. Download QuPath for: Windows, Linux, or Mac OSX.
Microscope-PiCam is a free open-source web-based solution that acts as the soul of a Raspberry Pi based microscope.
It is an ideal solution for taking still images using a 12 MP HQ camera attached to a gemmological microscope.
The project has detailed instructions on how to setup your Raspberry Pi
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