Highligting the "Borders" of the Object to be classified


At the moment I am running Cellprofiler in order to classify Objects on images. Unfortunately it is close to impossible to “see” where exactly one object begins and the other ends.

This means that Cellprofiler will provide the outlines of the Object in a way that is sufficient for further use with Cellprofiler Analyst. However the manual sorting is neither accurate nor easy because it is difficult to see what I am actually sorting. It could be only Object A or it could be Object A and the nearby Object B together.
Is there a way to make Cellprofiler Analyst to show only the Object to be sorted? Maybe by showing everything else much darker?


I’m a a bit confused by your description as to what you’re seeing that is making it difficult to sort cells. Perhaps a screenshot of CPA would be helpful? Or a screenshot of the types of objects you are trying to classify?

In any case, there are a couple of tips to help with visually making things out:

  • For each tile shown in Classifier, there is a small square that appears in the middle of the tile. Whatever cell/object is under the tile is the one that is being classified. This is the case even if another object is visible off to the side of the tile.
  • If sorting cells, we typically set the object to be centered in the tile as the nuclei (rather than the cell or something else) since the nuclei are usually easy to make out and are well separated.
  • In CPA, you can adjust the color contrast of the tile by selecting View > Image Controls
    from the Classifer menu, and changing the “Contrast Stretch”. - Finally, you can add outlines to the list of images to display in CPA by saving them using SaveImages by set “Record file and path information…” to “yes”. In CPA, the outlines will then show up in the tiles as well.



no cells, corrosion on steel. In order to test anti-corrosion-coatings…

Thank you, this is what I was looking for!
now it works as it should :smiley:


Thanks for writing back!