A first introduction into CellProfiler.
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
To be able to follow the course you need to know basic image analysis:
- concept of “images are a matrix of numbers”
- handling of multi-channel images
- bit-depth
- segmentation by applying an global threshold
- “analyze particles” (connected component analysis)
- The course material was tested using CellProfiler 3.1.9. Download CellProfiler from https://cellprofiler.org/releases/
- watch the recorded course: https://www.youtube.com/watch?v=QrzHQIiIDKM
- This workflow solves the same image analysis question (and more) as my ImageJ/Macro Introductory course https://github.com/ahklemm/ImageJMacro_Introduction