Intensity Ratio Nuclei Cytoplasm Tool - Area Selection Error

[aabdallah94]

I'm trying to use the Intensity Ratio Nuclei Cytoplasm Tool but when I run it, I get an error and the message "Area Selection Required". I've tried with 2 different fluorescent channels and had the same issue.

[volker-baecker]

Hi @aabdallah94,

here is what I get:

Did you see the documentation on the wiki?

You need to have the two channels as two separate files in the same folder. Their filenames must be the same, except for the part that is the channel name or identifier. You have to enter the channel names or identifiers in the options of the tool (right click on the s-button).

I also changed the auto-thresholding method for the nuclei segmentation from the default method "Huang" of the tool to "Default", since the first one select too much of the low signal around the nuclei in the nuclei channel.

Your images appear to be RGB, but I suppose that your original images are grayscale? If not you need to convert them before using the tool.

These images also do not have a scale (pixel size) set. If your original images have, you should either adapt the min nucleus area or select remove scale in the options.

Does this help?

Best,
Volker