Creating a pattern from immunofluroscence images

Hello community,
I wish to create patterns such as concentric circles, by connecting the green dots (CD4 staining) (please see image below). Please let me know if there is a macro available to do this. I have multiple images.

Thank you

1 Like

Hey @Amrutesh_S_Puranik,

can you maybe explain your image analysis problem a bit more in detail? For example I’m not sure what you mean with “dots” in the CD4 channel. Also, do the red and the blue arrows point at the structure you are interested in? Is the DAPI channel relevant?

Furthermore, if you could share some original image data files, which we can open in Fiji for example, we could try out tools before recommending any.


1 Like

Dear Robert,
Thank you for your reply. Attaching the image that will open in Fiji. Please check for Channel 2 (CD4, green) and Channel 3 (DAPI, blue). I’m wondering if there is a way to map/identify a contour like pattern over green channel.

Thank you

122619_CD68_089_[10755,50896]_M2_component_data.tifFixed.tif (12.5 MB)

So you want to segment the green channel? Or do you want to segment the blue channel and show contours on the green channel?

I can use stardist to segment blue channel and thanks to your YouTube videos it works well. Contours on green would be great.

1 Like

So StarDist has the option to save the ROIs of the nueclei to the ROI Manager. Afterwards, you can switch to the green channel and activate “Show All” in the ROI manger to transfer the ROIs to that image.

Let us know if this solves your question.

1 Like