*** What in the world does this output measurement name refer to:*** “mean_Bacteria_Intensity_IntegratedIntensity_MaskGreen”, or “mean, Bacteria, Intensity_IntegratedIntensity_MaskGreen”?*
The first “mean_” is a bit complicated. If the measurement is from the Per_Image
database table, or the Image spreadsheet, then it refers to the mean of that measurement across all objects in an image. However, if the measurement is from the Per_Object table, then the output is for a Parent object from a Relate module with the setting for “… generate per-parent means …” set to Yes, and it refers to the mean of the measurement for all the children across that particular parent object. Then to make it even more complicated, you can have the Mean across all parent objects in an image, of the Mean of the children within a parent (this measurement would be named something like “Mean, , Mean__…”. (We have debated whether to even include these “means of means” as their scientific significance may be of only confusing value, but we have left them in for now).
“Intensity” is the measurement category
“IntegratedIntensity” is the intensity of the Bacteria object, summed across its extent. But note that since this whole measurement name begins with “Mean_”, then the single number (in the Per_Object table) is the average of the individual objects’ summed intensities
“_MaskGreen” refers to the input image, which is the Green channel with a Mask applied at some point
This CP manual page may help as well.
(Edit March 2019): See also our more recent description here: https://github.com/carpenterlab/2016_bray_natprot/wiki/What-do-Cell-Painting-features-mean%3F