Compute histogram of measurements from many images

cellprofiler

#1

Hello,

I have many images which contain similar objects.
Is it possible to draw an histogram of a particular measurement of these objects (e.g. area) for all objects in all images? Not just one histogram for all objects in each image…

Thanks for the information.

Kind regards,

Vincent


#2

Hi Vincent,

DataTools in CP are useful for analyses on aggregate data, i.e. across cycles. So, run CP to get your measurements (e.g. area), then use DataTool->Histogram, load in your output file and see if you can plot what you need this way.

David


#3

Hi David,

Thanks, it works.
But it seems there is no way to make datatool run from the pipeline…

Vincent


#4

Hi Vincent,

Indeed, you cannot run DataTools from a pipeline. The pipeline model of CellProfiler is constructed such that each image is processed independently (with a few exceptions, like CalculateStatistics). You could use the DisplayHistogram module, for example, to display a histogram from an image on each cycle, but to do any pre- or post-processing on all the images, you need to run a separate pipeline or DataTool. I agree with your implication that automating this sort of post-processing would be desirable, and We That Are CP have discussed new models like this for the next incarnation of CellProfiler, though it is still in development so I can’t say whether this will occur or not.

However, anyone is free to write their own “SuperHistogram” module which takes all cycles’ measurements into account and post it here!

Best,
David


#5

Hi David,

It is perfectly clear now about what can be done and what can not be done (I mean right away). Thanks a lot!

Vincent