Display image histograms



Is there any possibility to display the values on the image histograms as pixel values - not as µm or whatever it is.
And in addition, would it subsequently be possible to extract all those pixel values to a data file (txt or xls)?




In the DisplayImageHistogram module the pixels intensity values are displayed, however like all images in CellProfiler, the pixel values are normalized to range from 0 to 1. Note that they are intensity histograms, and do not denote lengths of any kind (you cited microns, which don’t make sense here unless I misunderstand your question). But you’d rather have the 0-255, or what ever bit-depth range your images are encoded in? That will likely not be a high priority alteration for us, but if you have the Developer’s Version, you can double-click on any plot and alter the tick marks to display whatever you want, to rescale to their integer intensity values.

As for exporting these values, I don’t know of an easy way to do this currently. With the Developer’s Version, you could try saving the plot to your workspace using Matlab’s plot tools, and manipulate it there. I will add this request to our ToDo list.