Cell segmentation, Classification and Spatial Analysis in Multiplexed Fluorescence Microscopy Image Data.
Trainer: Anna Klemm, BioImage Informatics Facility, SciLifeLab, Sweden
Authors material and data: Anna Klemm, Fredrik Nysjö, Lina Wik, Arne Östman, Carolina Wählby
License: BSD 3-Clause
April 2, 10:30 AM - 12:45 PM (2h 15min), Tutorial 1, Infante hall
10.30-10.50
Presentation: Overview of Multiplexed Fluorescence Image Analysis
10.50-11.00
Introduction to the material
11.00-11.15
Demo: Creating a QuPath project, cell detection
11.15-11.45
Intro to semi-automated cell classification and data export
11.45-12.00
Strategies for training cell classifiers
12.00-12.15
Using pixel classification to detect vessels
12.15-12:30
Spatial analysis in QuPath
12.30-12:45
Final remarks, outlook
Extra material: Inspecting multiple tissue cores using the BigDataViewer and BigDataViewer Playground in Fiji