Hi there,

quick question, is the IntegratedIntensity algorithm in the MeasureObjectIntensity module summing up all pixel intensities for the identified objects, or is it creating a median/mean and reporting it instead?




It calculates the IntegratedIntensity of each individual object, which is then written to the spreadsheet/database in a file/table that matches your object’s name; the window that’s popped up when you run the module reports the average of all the objects in that particular window.


Right, so when I ask it to export the IntegratedIntensity of my 2nd objects, and it reports e.g. 21.365007 for 11 primarily identified objects, the 21 is an average over all identified objects? (Sum of all divided by number of identified?)


Which spreadsheet/table are you looking at? The “Image” sheet/table will report an average of the 11 objects; the sheet/table of your secondary objects should report a value for each individual object.


I’m looking at the table for the secondary objects (MitoTMRM-Intensity-IntegratedIntensity). But I’m only getting one value per image:


Maybe you can send along the pipeline and/or your output tables to help clarify this, but the screenshot you just posted looks to me like an image table- there’s no “ObjectNumber” column, there’s a “count” column, and all the ones where there’s a count of 0 have nans in the mean/median columns which makes me think those are the means of object measurements.


Damn found my error (and the other tables). Thanks for clarifying it!
On a different matter… to calculate an overall background for the pipeline, would it be appropriate to calculate the background for each photo (by masking the signal) and taking the average (from all photos) for the pipeline?