Specify cell colors (cluster ID) of segmented objects



Hi there,
I’m using a CellProfiler workflow to segment DAPI stained nuclei (using IdentifyPrimaryObjects) and measure a number of morphological features. I export a table (using ExportToSpreadsheet) in which columns represent the different calculated features, and rows represent each cell. The imageID and the cellID are provided in the table, which is great, however I want to view the relationship between these cellIDs and the image file.
This is because I’m using the spreadsheet data to perform a cluster analysis, and each cell gets assigned to a cluster. In order to validate the clustering I’d like to be able to go back to the image of the segmented nuclei, and assign all cells from a given cluster to a given color. (Currently I believe colors are assigned at random based on the segmentation?)

In Fiji, using ROIManager cell indices are shown, and you tell the ROIManager to assign all ROIs from a list of indices to a given color. Is there something similar in CellProfiler? I don’t know how to view the ObjectNumber (from IdentifyPrimaryObjects) on the image with the objects, nor do I know how to assign specific Objects to a given color.

thanks for your help!


Hi Amanda,

I’m not sure if I totally understand what you are trying to do but I think these two module uses might help.

  • The DisplayDataOnImage module can be used to display the object number on your output images. If you select your objects as your Input Objects it will give you the option to display the Object_Number on an image. So this will allow you to know which object ID is which in the spreadsheet.

  • Another useful one is ConvertObjectsToImage. You can use this to output your segmented objects in grayscale (where you could put it into FIJI and apply an LUT) or apply a colormap of your choice to your image within CellProfiler.

Hope this might help!