I’m a relative newcomer to CellProfiler but enjoying experimenting! My ultimate goal is to estimate the proportion of spleen surface on H&E stained slides made up of white pulp. I have a pipeline which takes some input images from which it extracts metadata through a regular expression (with brackets around the section containing the metadata). These images are processed (and therefore become new images), before an object (the spleen!) is identified and measurements taken.
When I look at the object measurements each measurement has an image and object index, but the image metadata has not come through, despite ticking “add image metadata to columns to your object data file”.
I wonder if this is because either: 1) I am not succeeding in extracting the metadata (though the regexp test works fine); or 2) because I am working on secondary images, not the primary ones, maybe the metadata does not get transferred through.
Any advice would be appreciated, and I can provide more details is necessary.
Thanks in advance,