PiV – Patologi i Vest’s First Hands-on QuPath Workshop!
PiV hosted its very first hands–on QuPath workshop. Let's see how it went!
Last week, PiV hosted its very first hands – on QuPath workshop, organized by our team leader Sabine Leh. The workshop was led by Radwan Etwebi, a medical student and QuPath expert, enthusiast, and warrior. The success of the workshop owes much to Jennifer Janani Antonythasan, a master's student in the PiV project, whose meticulous preparation of a manual made the entire event possible.
The workshop consisted of three concise 30-minute sessions during which a group of pathology residents were introduced to the world of QuPath. The task was to train an object classifier in Ki67 stained neuroendocrine tumors and apply it to new test images to determine the Ki67+ percentage for each image.
Here is a peek into the agenda:
Monday:
(A) Download relevant files.
(B) Create a project & add image.
(C) Create full image annotations.
(D) Manually annotate for tumor/non–tumor areas.
Tuesday:
(E) Carry out positive cell detection.
(F) Train an object classifier.
Wednesday:
(G) Apply "positive cell detection" and the trained object classifier on test images.
(H) Score Ki67+ percent for each of the 4 test images.
Making learning fun, participants engaged in a friendly competition to find the Ki67+ percentage closest to the ground truth. Three winners emerged, each earning a sweet reward – a delectable bar of chocolate.