UCT PathSlides

UCT PathSlides is a Python + Flask web app, used to display extremely high-resolution histology slides and quiz anatomical pathology students. (A login is required to view it.)

This is a complex project that involved many steps:

  • Digitising the histology slides using an Olympus VS120 virtual microscope.
  • Converting the huge digitised slides from their proprietary Olympus .vsi file format into the more open BigTIFF file format. (Using Bio-Formats command line tools.)
  • Converting the BigTIFF files into image pyramids.
  • Coding the web app, using the Flask framework, Bootstrap and MySQL.
  • Integrating the Leaflet open-source Javascript library to display the zoomable, interactive histology slides.
  • Connecting the app to SendGrid, so that students get emailed when their comments are moderated by the professor.
  • Deployment via DigitalOcean, which included setting up an Ubuntu droplet and a SSL certificate from Let's Encrypt.

All in all a really valuable learning experience.

Image of UCT PathSlides
Image of UCT PathSlides
Image of UCT PathSlides