Workshop material

In the first part the workshop takes a quick tour of the different tools available in QuPath. In the second part the tools are used to analyze fluorescence and IHC images. The aim of the workshop is to help the participants getting started to use QuPath for their image analysis projects, to understands the methods applied and the results obtained and to avoid possible pitfalls.

Program

1. Project creation

2.

After the session you will be able to built your own CellProfiler pipeline, including:

• Image data import
• Object segmentation (e.g. detect nuclei in an image) using the modules "IdentifyPrimaryObjects" and "IdentifySecondaryObjects"
• Object feature measurements (e.g. measure size, shape and intensity of cells)
• Measurements export to a spreadsheet
• Creating and saving quality control images

Workshop session about sharing and licensing materials such as [raw] data, manuscripts, code, slides. The slides cover the FAIR principles, terminology such as authors, copyright holders, licensees.

The one-day course is focused on processing microscopy images showing cells and nuclei. We will dive through segmenting objects, measuring their properties, managing measurements in tables and plotting results.

A lecture about challenges and solutions for GPU-accelerating bio-image analysis workflows and running them in the cloud.