Pathology - MEDevel.com: Open-source for Healthcare, and Education

Healthcare

The Challenges of Open-Source Healthcare Tools: A Lack of Reliability, Updates, and Maintenance

Open-source healthcare solutions promise cost reduction and customization, potentially revolutionizing the industry. However, users of tools like EMR, PACS, Radiology, and LIMS face challenges finding reliable, updated solutions. Many open-source healthcare tools are outdated or abandoned, lacking frequent updates. This situation frustrates users seeking well-maintained options, hindering the full realization

Healthcare

The Stagnation of Open-Source Medical Solutions: A Call for Innovation and Community Support

For years, the field of open-source medical software has seen limited innovation, with many projects becoming stagnant or receiving only minimal updates. Despite the increasing demand from users and countries, especially in low-resource environments and developing countries, to leverage open-source solutions, there has been a noticeable gap in the development

Pathology

18 Free and Open-source Whole Slide Imaging Pathology Projects and Libraries, a Comprehensive Guide for Bioengineers and Bio Data Scientists (2024)

Digital pathology is a cutting-edge field that transforms traditional pathology by digitizing glass slides into high-resolution whole slide images (WSIs). These WSIs capture the entire tissue sample on a slide, enabling detailed analysis and diagnostics through digital means. By using advanced imaging techniques, digital pathology allows pathologists to view, analyze,

research

Inviwo is a software framework for rapid visualization prototyping (3D HGistopathology)

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

Microscope

Microscope-PiCam: An Open-source Raspberry Pi Microscope

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

Pathology

OpenFlexure is an Open-source 3D-Printed Low-cost Microscope

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

RaspberryPi

MicroscoPy: Build Your Own Low-cost Digital Microscope using Raspberry Pi

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

Education

The Human Protein Atlas is What every Medical, Human Biology Students and Scientist Need

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

Open-source

Collaboratively Annotate large-scale DeepZoom images with MicroDraw

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

Development

18 Frameworks, Libraries, and Projects for Building Medical Applications

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.

Pathology

10 Open-source Whole-Slide Image Viewers and Analysis Programs; Redefining Digital Pathology

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

Pathology

Open Microscopy Environment (OME): Digital Pathology Redefined with Open source

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,

Pathology

OpenSlide: The Whole-Slide image processing library that stands behind most of Digital Pathology Projects

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.

Visualization

BioImageXD: Open source Microscopy Imaging Software

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

Pathology

Cytomine: Free Open source Web-based Digital Pathology (WSI) solution with Machine learning flavor

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

Pathology

Orbit: Digital Pathology meets AI (Machine learning & Deep learning) & Big Data with Open-source flavour

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

Pathology

QuPath: Free Open source Digital Pathology Whole Slide Viewer, & Analysis Software

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