I ranted against open source in the past. Yet this month I signed on as an external consultant and digital pathology expert for Cytomine. More on that conversion later.
In this post, I want to give an overview of what publicly available open source software there is. But wait, PMA.start from Pathomation is free of use, but it’s not open source; it’s closed source. So are the many proprietary viewers for the respective scanners our there.
Therefore the (somewhat clumsy) title of this post: it’s an effort to keep track of all things free to use in digital pathology. Know of a toolkit not listed? Let me know so I can add it!
The list (for whole slide imaging applications)
| Thumbnail | Project | Availability | Open / closed |
|---|---|---|---|
 | CellProfiler | Open source | |
 | Cytomine Community Edition (U Liege) | Github, PyPI, Wiki | Open source |
 | PMA.start (Pathomation) | PyPI, Wiki, YouTube | Closed source |
 | QuPath (U Edinburgh) | GitHub, ReadTheDocs.io, YouTube | Open source |
| TIA Toobox (U Warwick) | Github, PyPI, ReadTheDocs.io, YouTube | Open source | |
| DP LabTools (U Toronto) | ReadTheDocs.io | Open source | |
| OMERO (U Dundee) | ReadTheDocs.io | Open source | |
 | ASAP (U Radboud) | GitHub | Open source |
Software libraries (for developers only)
The following libraries are used often when developing new digital pathology software packages from the ground up. Note that we’re not including trivial references like SkLearn or TensorFlow.
This is a reference list for developers only. Meaning: an end-user has no use whatsoever in getting OpenSlide and staring at a bunch of .dll files. Duh.
| Library | What is it? | Languages | Documentation |
|---|---|---|---|
| Bio-formats | |||
| OpenSeaDragon | “An open-source, web-based viewer for high-resolution zoomable images, implemented in pure JavaScript, for desktop and mobile.” | ||
| OpenSlide | “a library that provides a simple interface to read whole-slide images (also known as virtual slides).” | C, Java, Python | Wiki |
Viewer software
The following is a list of proprietary but free viewers. I limit the list to the viewers only, as they’re usually free to download and come with few or any restrictions (RUO is the most common disclaimer encountered) E.g. we include NDP.view from Hamamatsu in this list, but not the server-based NDP.serve solution. Likewise, we list Aperio ImageScope, but not Spectrum’s e-Slide manager.
| (Scanner) vendor | Software | Screenshot |
|---|---|---|
Even more software
The following software packages are more general purpose than the above, but at the same time still frequently used for various purposes in the context of digital pathology.
| Thumbnail | Project | Wat is it? | |
|---|---|---|---|
| Icy | |||
| FIJI (ImageJ) | |||
 | OMERO (OpenMicroscopy) | ReadTheDocs.io | |