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!