The 2nd and 3rd inputs into cellsegm.segmct are the minimum minN and maximum maxN nucleus thresholds, respectively.
minN is explicitly stated as 0.038.
maxN is calculated according to the equation ((4/3)*(pi)*(Z/2*0.4)^3), which calculates to 0.0335.
Rather said, maxN is less than minN. This leads to exclusion of every nucleus in cellsegm, and creates errors downstream in the pipeline.
For example, I was getting an error at line 162 of rnascope_mouse.m:
Error using save
Variable 'excel_dots_of_ROI' not found.
Error in rnascope_mouse (line 162)
save([filename(1:end-4),'_dots_of_ROI.mat'],'excel_dots_of_ROI')
When I changed the maxN threshold to 100, the full pipeline ran fine without error.
I'm posting it as an issue instead of a pull request because 1) I don't know the appropriate maxN for all cases; each user should set it themselves and 2) so other users will see it.
There's an error at the above-mentioned place in rnascope_mouse.m using the default settings. Line 66 is:
[cellbw1,~,~,~] = cellsegm.segmct(ch,(0.038),((4/3)*(pi)*(Z/2*0.4)^3),'prm',prm);The 2nd and 3rd inputs into
cellsegm.segmctare the minimumminNand maximummaxNnucleus thresholds, respectively.minNis explicitly stated as 0.038.maxNis calculated according to the equation((4/3)*(pi)*(Z/2*0.4)^3), which calculates to 0.0335.Rather said, maxN is less than minN. This leads to exclusion of every nucleus in cellsegm, and creates errors downstream in the pipeline.
For example, I was getting an error at line 162 of rnascope_mouse.m:
When I changed the
maxNthreshold to 100, the full pipeline ran fine without error.I'm posting it as an issue instead of a pull request because 1) I don't know the appropriate
maxNfor all cases; each user should set it themselves and 2) so other users will see it.