BioCampus workshop: What you need to know about QuPath for fluorescence and IHC images analysis¶

Proposed by Montpellier Ressources Imagerie¶

Trainers:

  • BAECKER Volker
  • BENEDETTI Clément
  • HASSEN-KHODJA Cédric

Requirements: Requirements & installation guide

Program¶

1. Project creation¶

  • Lecture

  • Slides

  • Ex 1: Creating a new project

  • Ex 2: Sharing a project

  • Ex 3: Organizing the images in a project

2. Navigation, Annotations, Measurements¶

  • Lecture

  • Slides

  • Exercise

3. Stain Separation / Color Deconvolution¶

  • Lecture

  • Slides

  • Exercise

4. Tissue segmentation and classification¶

  • Lecture

  • Slides

  • Ex 1: Fully manual segmentation

  • Ex 2: Using a threshold pixel classifier

  • Ex 3: Using a N-classes pixel classifier

  • Ex 4: Semi-automatic segmentation using SAM

  • Ex 5: Segmentation quality control

  • Ex 6: Area of signal per slide

5. Cell Detection¶

  • Lecture

  • Slides

  • Ex 1: QuPath built-in method

  • Ex 2: Use StarDist in QuPath

  • Ex 3: Segmentation quality control

  • Ex 4: Use CellPose in QuPath

  • Ex 5: Use InstanSeg in QuPath

6. Cell Classification¶

  • Lecture

  • Slides

  • Ex 1: Using a threshold object classifier

  • Ex 2: Using a N-classes object classifier

7. Multiplex Analysis¶

  • Lecture

  • Slides

  • Exercise