This uWorkshop intends to give a brief introduction (Teorical & Pratical) to the use of QuPath (free open-source software for "Quantitative Pathology") for analysis of tile & stitched large image datasets, such as those obtained in the IGC's slide scanners from the Histopathology and Advanced Imaging Units (Hamamatsu and Zeiss Imager Z2).
The workshop will include:
1) Brief introduction to image analysis basic concepts
2) Brightfield vs fluorescence, and RGB vs composite images; color models and separation/deconvolution
3) The concept of tile & stitching and pyramidal image datasets
4) Image segmentation
5) Classification with machine learning
6) Data visualization and representation in QuPath
7) Hands-on Sessions in QuPath
8) A brief introduction to groovy workflows and QuPath extensions
REQUIREMENTS: Students must bring their own laptop, transformer, mouse and must have had previous contact with ImageJ/FIJI at a basic level.
DATES AND LOCATION: The workshop will take place in the Protagoras room (IGC's Library building) from 1 to 2 of June.
There is a limit of 20 participants!
Applications close 26th of May, 2023.
For more information, please contact:
Patrícia Rodrigues: parodrigues@igc.gulbenkian.pt
Mariana Ferreira: marianaferreira@igc.gulbenkian.pt