Identification/labelling of single cells withing an image

Hi there,

I am currently using CellProfiler version 1.0.5811 Compiled on MAC OS X. The pipeline is working great for my purposes: It identifies the nuclei as primary object, cell border as secondary and then mitochondria as second primary object. My problem is that I have around 10 cells per image and would like to know to which cell the extracted features correspond to. The extracted measurements are stated in the cvs file as corresponding to cell 1, cell 2, etc… but I would need to identify which particular cell in the image does CellProfiler refer to (1, 2, etc…). How can I do this? to automatically “label” each cell and to hopefully even export an image that allows me to identify to which cell the measurements correspond to.

I send you in attach and example of the pipeline and two images (channel one tag-blue: C=1; channel two tag-green: C=2). Hope its helpfull.

Thank you so much in advance and looking forward for good news. :smile:

All the Best,

YR_070909_binaryPIPE.mat (2.28 KB)


If you still using CP 1.0, then unfortunately, there is no way to display this information on the image. However, if you upgrade to CellProfiler 2.0, then you can do so.

Attached is your pipeline, upgraded for CP 2.0 which includes the module DisplayDataOnImage (before the first SaveImages) which will do what you want.

YR_070909_binary.cp (19.3 KB)