I am trying to geht QuPath running for my purposes and think I could get some conceptual help from you guys:
I am working with (multiple) TMAs and AEC as the IHC chromogen. Overall goal is to calculate number of positive cells for any given stain in an area of interest (tumor vs stroma) and batch analyse all TMAs within the same project.
So far I have manage to
- set stain vectors, pos. cell detection parameters
- de-array TMAs
I am joyfully reading the posts from Research_Associate like:
as well as Pete´s blog posts and the Youtube videos.
However, I am struggeling a bit currently to define a logical hierarchy of actions for my workflow like “what to do first”:
Idea currently is:
- Creating project
- Importing all images or keeping TMAs individually ?
- Setting stain vectors equally for all images
- De-Array TMAs
- I guess I don´t need Tissue Detection since I am working with TMAs.
- Area identification / Classification: As I´d like to get pos cells in a given tissue category (tumor / stroma), I imagine this needs to come first. So would you use Reasearch_Associates workflow with the SLICs or the pixel classifier to get tissue areas? Would you use Analyze->Calculate features for this ?
- Positive cell detection
- Analzye all TMA cores / all TMAs
- Use sth like https://petebankhead.github.io/qupath/scripting/2018/03/05/script-annotation-results-merge.html
for merging annotations and exporting
Thanks for your input