Analyzing in cell analyzer images for cell morphology identification(nuclei, cell, actin etc)


Hi all,

I’m trying to analyze incell analyzer images for cardiomyocite morphology study. I want to get information about the nuclei, cell itself and actin at this point. Cell are stained with DAPI, Cyt3, Cyt5 and FITC. I’m using the the pipline shown in the link below, and images below. DAPI gives information about the nuclei (thus number of cells) and FITZ about actin(thus I can get information regarding the cell boundary, and also cell shape in general). However, DAPI and FITZ images are separate and makes identifying primary, secondary and tertiary objects difficult.the pipeline pciks onlyone image(in this case DAPI image), and identify the secondary and tertiary object based only on this image. My question: Is it possible to merge two and or more images (in this case DAPI and FITZ images) to get information regarding the nucleus(cell number) and actin(cell boundary & morphology)?
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Acurate_segmentation.cppipe (11.6 KB)

Thank you in advance fro your help.




Please try to first fix the issue of correctly naming images for corresponding channels.
In your module Metadata, the regular expression was not set correctly to the names of your images, e.g. A01fld1DAPI
You can actually skip that Metadata module (Extract metadata : No)
Then in you module NamesAndTypes

Make “File__Does___Contain__DAPI” = DAPI_channel
Make “File__Does___Contain__FITC” = FITC_channel

After having correct DAPI image named “DAPI_channel”, FITC image named “FITC_channel”, etc. >> in your module IdentifySecondaryObjects : choose “Select input image” with “FITC_channel”, then the total actin area of the cell will be identified correctly.

You may find some good advices from Beth here

As for : "Is it possible to merge two and or more images"
Yes, we have module called ImageMath in which you can choose the operation Add to make the merge.