Filter/Select objects by mean signal intensity of each obj?

Dear All,

I’m wondering after I identified the primary objects from image, can I filter/select objects that are above a certain mean signal intensity?

This way, I can first identify objects with a loose threshold and then select the ones that meet certain mean signal intensity criteria.

This would be particularly useful when the pixel signal intensities within the objects fluctuate significantly.

Thank you very much for any input.

You can use the FilterObjects module for this purpose. If you apply the MeasureObjectIntensity module beforehand, you can specify the per-object mean intensity as the measurement to filter with and then specify a cut-off value that each cell has to exceed/fall below.

Regards,
-Mark

Thank you very much, Mark. This is really helpful.

I found Cellprofiler really powerful for 2D images even though I only started 1 week ago. It’s a great job to make an open software so comprehensive.

I heard you guys are also working on a version that can handle 3D stacks?

True, this is on our roadmap. However, adding this functionality is pretty far down the line: github.com/CellProfiler/CellProfiler/issues/524
-Mark