Publikationsdatenbank

QuPath workshop:
learn how to use open source software for quantitative pathology and bioimage analysis (2023)

Art

Poster

Autoren

Mikulski, Zbigniew

Klopfleisch, Robert (WE 12)

Aubreville, Marc

Kongress

Annual ESVP/ECVP Congress 2022

Athen, 07. – 10.09.2022

Quelle

Journal of comparative pathology

Bandzählung: 203

Seiten: 42

ISSN: 0021-9975

Sprache

Englisch

Verweise

URL (Volltext): https://www.sciencedirect.com/science/article/pii/S0021997523000373

DOI: 10.1016/j.jcpa.2023.03.011

Kontakt

Institut für Tierpathologie

Robert-von-Ostertag-Str. 15
14163 Berlin
+49 30 838 62450
pathologie@vetmed.fu-berlin.de

Abstract / Zusammenfassung

This workshop aims to give participants a better understanding of how to use QuPath for image analysis. We will cover the most common analysis tasks, and teach how to use convenient tools for manual counting and measurements of the length and area of different structures. We will use QuPath’s commands for automated cell counts in H&E and immunohistochemistry (IHC) slides. With the help of machine learning, we will teach the software how to perform object and pixel classification, which is very useful in complex and difficult samples. We will also perform measurements of IHC-stained areas. All of these analyses can be easily adapted for immunofluorescence and multiplexed slides. We will present an outlook for the future, share examples of implementation of deep-learning workflows, and show how QuPath can help to improve the reproducibility of image analysis. Attendees will go home with knowledge and workflows that they can adapt to analyse their own tissues and stains.