Use of subset of images within a file

cellprofiler

#1

HI, First, thanks for this terrific tool!!!

I have been working with CP3 for some time now and I find it very useful and powerful for our needs. However, I have been struggling with some issues…
For example, I would like to use CP to analyse FRET time lapse recordings (2 channels for FRET (donor & acceptor) per confocal image, every given interval --> a huge tiff file).
So, in order to get offline analysis of FRET dynamics, I would like CP to measure fluorescence of objects for the entire file, take care of the background, etc. That I can do. :wink:
But then, I would like CP to take a subset of the images within the file (I can specify which images i.e. t = 1 to 5) identified as baseline and isolate values for these images and then do some calculation (I can take care of the calculation part too).

So, to make a big story short… Can CP use a subset of images (or frames) within a file, identify them and use the data later in a pipeline? And if so, how?
I tried in the “NamesAndTypes” module (using criteria like t < 5 to differently name images) or by grouping to identify let say images from time 1 to 5, but it doesn’t work. I have no experience in coding or python whatsoever…

I would greatly appreciate if someone could help me!

And actually, the ability to use a subset of images within a file would be very helpful to several other applications I have…

Thanks a lot!!

Jonathan


Slicing based on Metadata info
#2

Hi,
No, there’s unfortunately no way to do this sort of “looping” within a pipeline- ie first run images 1-5, do a calculation, then start again and do the whole stack based on the first loop. I’m afraid the only way to do it is to do your baseline calculation first and then pass the value into CP, either manually entering it somewhere in the pipeline or by passing it as a piece of metadata (ie do this for all of your movies, create a CSV with the movie name and calculated baseline for each movie, then upload that into the Metadata module). I totally get the desire for the functionality (I’ve wished for it once or twice myself :wink: ), but it would be pretty difficult to implement from a software point of view. Sorry!


#3

Thank you very much bcmini!
I really appreciate all your (and the team) work on CP and I understand that such feature could be hard to implement! And thanks for the advice!

Best,

JLx