Accessing images / object thumbnails from per-Object scatterplot data points?


#1

Hello!

Is there a way to quickly access images or object thumbnails from per-object scatterplots in CPA?

I know I can create a gate and right-click -> show cells/images in gate but 1) I would prefer not to have to create a gate every time and 2) It seems that when fetching the gated images or objects, previously instated filters do not apply, and I get objects that may not be visible on the scatterplot.

Thanks!


#2

@Fabba123
Unfortunately, that functionality does not exist. I would encourage you to make a feature request on GitHub where the CellProfiler developer community can see it. Follow this link and file an issue.


#3

I have a similar question as Fabba123 and was wondering if there was a work around.

Is there a way to scatterplot a subset of data, allowing you to “show cells in gate” for that subset? The “show cells in …” feature seems to ignore filters. It would be nice to be able evaluate my expt controls individually as a plot and with the “show cells in …” feature.

More simply, is it possible to retrieve images of all objects (as in the “show cells in gate” feature) that meet a set of criteria that is entered manually? For example Metadata_Well = H12 AND nuclei_Intensity_MedianIntensity_mCherry >0.008?

thanks!
Jason


#4

You can definitely create filters like that for viewing images in Classifier or in the ImageGallery; you can make the filters inside either of those using the dropdown usually set to “experiment”- though in my experience that can sometimes be slow, so you can also just write them directly into the properties file.

Good luck!