I’d be grateful for your advice please (I’ve just started using CellProfiler)
I would like to be able to identify with an image the proportion of macrophage cytoplasm occupied by carbon after phagocytosis. ie. we feed the macrophages carbon, then take pictures.
I have a pipeline which identifies cells, and identifies carbon. I use IdentifyPrimAutomatic, then Relate the two. The child objects are carbon clumps, and the parent objects are cells. I can output this to Excel or SQL. Excel gives me two object tables (cells and carbon). SQL shows only one (cells), and I cannot find a table related to carbon.
I would like to calculate the sum total of area of carbon clumps, and divide this into cytoplasmic area, giving a per-cell output.
So I have two problems:
- I cannot find the column in the Excel file which identifies “this carbon belongs to this cell”- does it exist?
- A missing table in SQL file (child objects)
I’m using CellProfiler version 1.0.7522 on Windows Vista.
Pipeline is attached with a single image.
Many thanks in advance for your help.
PBMCWithCarbonPIPE.zip (1.46 KB)