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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:

Mariana Ferreira: 


Start: 1 June 2023
End: 2 June 2023

Instituto Gulbenkian de Ciência (IGC), Rua Quinta Grande, Oeiras, Portugal

Rua Quinta Grande 6
2780-156 Oeiras Lisboa

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