QuPath: Quantitative Pathology & Bioimage Analysis Software

hands-on
software
imaging
live training

QuPath: Quantitative Pathology & Bioimage Analysis Software

Target Audience:
VIB PhD Student
VIB Postdoc
VIB Staff Scientist
VIB Group leader & Expert
VIB Technical support
Location:

Ghent - VIB UGent FSVM II

Duration:

18 October 2024, 9h30-16h30

General context

This one-day workshop is aimed to use QuPath, an open-source software for bioimage processing and analysis of slide scanner images.

A dedicated time will be used to analyze some of the participants dataset, so please contact the organizers if you would like to bring your own data to process/analyze.

Objectives
  • Overview of QuPath: manage images, annotations, general concepts
  • Cell Segmentation
  • Pixel classification
  • Feature extractions
  • Object classification
  • Basics of scripting in QuPath to batch process
Event intended for

This course is intended for researchers who are using or planning to use a slide scanner and would like to process and analyze their data.

Required skills

None. Participants are requested to bring their own laptop, QuPath pre-installed.

Software demonstrated

QuPath

Trainers

Benjamin Pavie
VIB Bioimaging Core, BE
Amanda Gonçalves
VIB Bioimaging Core Ghent, BE

Amanda is a Microscopy Expert at the VIB Bioimaging Core-Gent, where since 2011, she has gained expertise in large sample imaging and quantification, from slide scanner to light sheet. She also has over 15 years of experience teaching science, both practical and theoretical, on the graduate and post graduate levels.

Jérémy Verbeke
VIB Bioimaging Core Ghent, BE

Program

QuPath basic
-
QuPath scripting + User dataset analysis
-

Practical info

Location & Venue

18 October 2024

Ghent - VIB/UGent FSVM II

Technologiepark 75
9052 Zwijnaarde
Belgium

Public transport

18 October 2024

Ghent - VIB/UGent FSVM II
Public transport

From Ghent Sint-Pieters station, you can take bus 49, 50 or 70 to Technologiepark. Please check Routeplanner De Lijn for schedules.

Route description

18 October 2024

Ghent - VIB/UGent FSVM II
Parking

Route description

There is only one entrance to Technologiepark. At the entrance, please take a ticket and have it validated at the reception desk of the FSVM building. Parking will only be allowed in regular parking spots (for instance in front of the building) and in the new parking tower. Parking alongside the roads or in other places where there is no regular parking is prohibited and after initial warnings, fines will be issued (€ 50).

Venue contact

18 October 2024

Ghent - VIB/UGent FSVM II
Extra information

Room: L4 - on the fourth floor