Hi, sorry for the delay. You are very close I think, but in any case try out the attached pipeline!
This one is easy, and you’ve already done it. Just look in your output spreadsheet for the object in question, namely MaskedPuncta (assuming you want only masked puncta sizes). There is a column named “AreaShape_Area” which has the output from the MeasureObjectSizeShape module, and the measurement Area.
For this, I added the module MeasureObjectIntensityDistribution, which was just recently renamed from MeasureObjectRadialDistribution. The output looks like this:
** BUT note that the pipeline I attached will only work in the Beta CellProfiler we recently pushed out, as there have been a number of fixes and added visualization in MeasureObjectIntensityDistribution that I thought you’d like. Download it here: cellprofiler.org/releases/
- I added ColorToGray simply because I only had your color image to work with
- I duplicated your IdentifyPrimaryObjects and changed a couple parameters, and disabled the original. I don’t think the smoothing is likely necessary and am using the raw DNA as input. I lowered the min diameter which was very close to the bottom nucleus size. I raised the Threshold Correction Factor to make the segmentation tighter around the nuclei
- I think you were missing too many puncta, so I changed to using Otsu thresholding method, and manually setting some declumping parameters
- I like your masking
- Added MeasureObjectIntensityDistribution. There are two ways to set this, scaled or unscaled. I did both as an example. Read the Help for more info.
Hope that helps!
lysosomes_structures_DLogan.cppipe (19.8 KB)