In an earlier live, I’ve written about the use and applications of open source initiatives in digital pathology. In the article, I spent a lot of time on total cost of ownership (TCO), and on the hidden costs of open source in particular.
About a year later, I’ve joined a hybrid commercial / open source initiative myself. What gives? Have I totally lost my mind? Or have I somehow sold out?…
Not exactly. Let’s just say that my thought process has evolved since the original article, and that there may be more virtues to digital pathology than I originally foresaw.
Open source microscopy
Open Source software comes around in different ways, but here’s one particular path in which it can happen, and how at least several (if not all) open source digital pathology has come around: OpenSlide

Despite its popularity and name-recognition, there’s one dirty secret to OpenSlide: it’s a progamming library; it’s not a download-install-point-click interface. It doesn’t come with a user interface. Come to think of it, it’s actually missing a couple of other features as well, such as tile representation (you can only extract regions from a WSI). Bottom line: the learning curve for OpenSlide is steep if you’re only used to working with commercial COTS like vendor-specific viewer software, Aperio eSM, VisioPharm, or HALO.
if you’re looking for more interface and user-friendly software, here is a (non-exhaustive; if you know of other projects, let me know) list:
A more comprehensive list is available at medevel.com, and another one (not limited to open source software) is maintained by the people at PathPixel (incidentally I named my own company Pixel Path, before I even knew these guys existed).
Datasets
Looking for sample slides? Here are a couple of source to easily retrieve slides from:
