Void area in B-catenin analysis & Matlab integrated in cellprofiler (?)




I am trying to analyze the effect of a toxin in cell junction (stained with a B-catenin antibody). In order to do this, I created a CellProfiler pipeline that basically creates a threshold (ApplyThreshold module) of my B-catenin image following a MeasureImageAreaOccupied module. The output of this pipeline is AreaOccupied, Perimeter and TotalArea. The output data from this pipeline (area or perimeter of the fluorescence) is not correlating very well with my images. In fact, I would like to only quantify voided areas. How can I analyze voided areas in cellprofiler version 2.2.0 (can’t use further versions)? Do you have any suggestions on how to improve my analysis?

Also, I would like to know if I can integrate a matlab script into cellprofiler v.2.2.0.

Thank you for your help!


Hi Pamela,

Can you please share your image with me? One thing you try is to convert binary image after thresholding into objects and using Convert Image To Objects modules to measure area occupied by those objects. Let me know if that helps you.


Hi Hamdah,

My apologies for my late response. I have tried your suggestion before or at least something similar. I am sharing a couple of images with you regarding my problem and the CP pipeline.

  1. Bcatenin: this is the image that I would like to measure

2)CP v.2.2.0 pipeline in use: this is the pipeline that I am using to analyze (measure) my image.

3)The pipeline in 2) generates the following Threshold image

  1. The pipeline in 2) measures the Threshold image in 3) and gives the following numbers. I am still trying to understand the meaning of area occupied and perimeter.

  2. I am interested in measure ONLY void areas (closed areas like cells, not every line in the image), like in this Matlab generated skeleton. Can I actually integrate a Matlab script into CP 2.2.0?

I really appreciate any advice or suggestion you can provide!

Thank you for your help!!


This is the image that did not upload, sorry. Thank you!