"Set interactively" applied to ALL images of different name

cellprofiler

#1

Hello,

I would like to use the sliding rule to “Set interactively” (in IdentifyPrimAutomatic) the threshold only once, and apply it to not just all the images with the same naming, but ALL the images identified with multiple file names. Is this possible? More details below if that’s unclear.

Many thanks,
ilan

Because I’m having CP identify files with 12 different labelings (ie the output files representing the 12 columns of automatic confocal 96well image acquisition - Incell3000), my pipeline looks like this:
SpeedUpCellProfiler
LoadImages
LoadImages
LoadImages
Resize
Resize
Resize
Resize
Resize
Resize
Resize
Resize
Resize
Resize
Resize
Resize
IdentifyPrimAutomatic
IdentifyPrimAutomatic
IdentifyPrimAutomatic
IdentifyPrimAutomatic
IdentifyPrimAutomatic
IdentifyPrimAutomatic
IdentifyPrimAutomatic
IdentifyPrimAutomatic
IdentifyPrimAutomatic
IdentifyPrimAutomatic
IdentifyPrimAutomatic
IdentifyPrimAutomatic
MeasureObjectAreaShape
MeasureObjectAreaShape
ExportToExcel
ExportToExcel
…For thresholding, I would like to use the Set Interactively function, but want to then apply that threshold to all 12 “IdentifyPrimAutomatic” modules automatically.


#2

Hi Ilan,

Unfortunately, that’s not a feature that CellProfiler supports at this time. If there is some demand for such a feature, we’ll consider adding it.

Is using an absolute threshold an option for you?

Regards,
-Mark


#3

Hi Mark,

Yes I’ve used that successfully for many analyses. However when I use different reagents/markers/GFPs in the exact same experiment I see there are intensity fluctuations and it would be great if I was just queried at the beginning of each analysis how I wanted the threshold set.

This would also be useful if there are natural fluctuations between experiments, perhaps due to subtle changes in laser strength, plates, temperature, etc.

Ilan