Percentage of Positive cells for a given dye


Dear Team,

I’m trying to analyse the following files. The Alexa 546 is an image for cell cytoskeleton, DAPI for the nuclear staining and the FITC is the one for some particles. I am wondering how can I quantify the percentage of cells with FITC labelled particles. … bEN4dnc9PQ … VlZjR0E9PQ … VFkwTVE9PQ

I’m attaching the pipeline that I’m using with this message and I shall be grateful if you could help me modify it inorder to quantify percentage of FITC positive cells.

Nanoparticle_analysisPIPE.mat (1.23 KB)


Hi Hemant,

Your pipeline is fairly close to what it needs to be (are you using the developer version?). I would add the ClassifyObjects module at the end which you can use to categorize which cells have particles. You would specify the Cells as your object, “Children” as the feature, and “1” as the feature number (which refers to the number of children determined by Relate), use “Custom-defined bins” and set the next setting as a single number, which is the threshold for the number of particles to be present in a cell for it to count as FITC-positive.

I would also downsample your images, either beforehand by adjusting the camera resolution or within the pipeline by using the Resize module. Provided that this is the only purpose you are putting them towards, they are far larger than they need to be.



Thank you very much Mark! I’ll try it again.