Introduction to QuPath -2nd Edition

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Instituto Gulbenkian de Ciência Rua da Quinta Grande, 6 2780-156 Oeiras

This Workshop 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: [email protected]

Mariana Ferreira: [email protected] 

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