Something wrong in "Area ratio for brightfield image"

cellprofiler

#1

Dear all.
A couple of years ago we received an estimated help here with a pipeline for our needs. In order to get not only blue detected region ratio we made some modifications of that pipeline. However, when for estimation of the pipeline we try some pure red o blue fragments the result is nonsense. The pure red or blue fragments appear plenty of…! its contrary color. What could be wrong in the pipeline?
Thanks in advance.
Konstan
ra|144x148aracc


DL_area_ratio_mio.cppipe (11.0 KB)


#2

Hi,

You have to calculate Percentage area occupied by blue and red segmeted region versus total area of image what you were calculating in a pipeline was area occupied by blue and red regions by their total area that is why you are not seeing any differences. Let me know if that answer your question


#3

Hi,
Yes, we need to calculate blue and red vs total area. So, what I have to change in my pipeline? On the other hand, how can I get in a data file only file names and % of interest areas? Because In my pipeline I have many innecessary columns. Thanks for help.


#4

Hej,
you can try to select the data in the ExportToSpreadsheet module. there should be the option to select the data to export.

I’m also interested in the answer how to calculate the percentage stained vs area complete.

Regards
Markus


#5

Hi,

I have made changes in your pipeline and added additional modules that can readily extract your desired measurements.
Good luck with your analysis

Regards
Hamdah

TJQuant.cppipe (9.2 KB)