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 Hamza Musa 10 Sep 2020 · 2 min read
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 Hamza Musa 9 Sep 2020 · 2 min read
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 Hamza Musa 3 Aug 2020 · 7 min read
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 Hamza Musa 1 Aug 2019 · 5 min read
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, Hamza Musa 29 Jul 2019 · 3 min read
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 Hamza Musa 28 Jul 2019 · 4 min read
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 Hamza Musa 24 Jul 2019 · 2 min read
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 Hamza Musa 21 Jul 2019 · 4 min read
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 Hamza Musa 14 Jul 2019 · 5 min read
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 Hamza Musa 3 Jul 2019 · 2 min read
