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BodenmillerGroup / cytomapper

R package for visualization of highly multiplexed imaging data
https://bodenmillergroup.github.io/cytomapper/
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Question for scale_bar for images used for publication? #77

Closed Pancreas-Pratik closed 1 year ago

Pancreas-Pratik commented 1 year ago

Good evening (afternoon here) :)

Maybe this is a silly/easy question? But just to make sure?

For publication/presentation, how do you guys produce the 100µm/250µm/etc... "scale_bar"?

  1. Is the DNA/nuclear staining channel used with searching the literature for what the nucleus size should be, and then a scale_bar measurement is added to the ROI section based on these two (actual nucleus size and reference literature nucleus size) together?

  2. or are H&E histology sections used (which I think have the measurement on the microscope images, as a reference?)

  3. or is there some other magical "automated?" way this is done to give the µm scale?

then the scale_bar is added afterwards?

Thank you for all the work you guys are helping us with at the Rosenberg-Nakanishi Laboratory in the UConn Health in Connecticut with all the tools you have and are coming out with.

nilseling commented 1 year ago

Hi @Pancreas-Pratik

this issue does not relate to the cytomapper package so I will only give a brief explanation. To add the scale bar you would need to know the physical size of one pixel. In IMC this is one micro meter. In flourescence imaging this is usually less. The microscope you are using usually saved this information in the image metadata and you can extract it with many commercial and open source software. Have a look online (Google) on how to extract this information from your images. Usually even FIJI is doing a good job with this.

nilseling commented 1 year ago

Closing due to inactivity