Save histogram plots?

Hi,
I would like to save the Histograms generated by the DisplayHistogram module, I can’t seem to find a way to do this in CP2.0. I tied to use SaveImages selecting ‘Module Window’ as image type, but this produces an error. It would be nice to be able to save the images produced in the windows for various modules.

Thanks,
Sam

Hi Sam,

Unfortunately, saving Module Windows has not been implemented. (We fixed the bug that produces the error when choosing this, but it doesn’t allow saving yet). It is on our list, but it is not as simple a fix as you might assume. Read more here, if you care to: github.com/CellProfiler/CellPro … t-33718926
Another tack is for us to retain the image for downstream saving in SaveImages, but this too hasn’t been implemented: github.com/CellProfiler/CellProfiler/issues/201.

The simplistic, non-high-throughput workaround is to click the save button in the toolbar of the module (looks like a floppy disk) and name the output. The only other route I could imagine, barring coding it yourself, would be to use RunImageJ and create a clever macro to save a screenshot of the module window. Though I expect this would be troublesome as it would be very sensitive to whether the display window was drawn yet, what cycle was being processed at that time in multi-processing scheme, etc. In any case, the proper implementation will have to wait for a while on our end, as far as I know.

Cheers,
David

Hi,

I was wondering if it was possible to save module windows yet? For example saving the DisplayHistogram output.

I am feeding individual XY well location tiff files in the input modules and each 3 channel XY location goes through the analysis modules, each well generating a DisplayHistogram among other things. I would like to save the graphs. Is there a better way of doing this in lieu of not being able to save the graph?

I note in SaveImages the option to save module/window in CP2.1.1 has been removed. There doesn’t seem to have been any bumps to the github discussions you linked to.

Kind regards,

Ed

Hi,

I was wondering if it was possible to save module windows yet? For example saving the DisplayHistogram output.

I am feeding individual XY well location tiff files in the input modules and each 3 channel XY location goes through the analysis modules, each well generating a DisplayHistogram among other things. I would like to save the graphs. Is there a better way of doing this in lieu of not being able to save the graph?

I note in SaveImages the option to save module/window in CP2.1.1 has been removed. There doesn’t seem to have been any bumps to the github discussions you linked to.

Kind regards,

Ed