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How to generate a markup file from ImageJ

PostPosted: Mon Dec 08, 2014 10:00 am
by cedric
Hey there,
i have just started to run 3B yesterday and i 2 questions about the markup file:

- What is the role of this markup file?
- Could anyone know how to generate a markup file with image J?

Thanks

Re: How to generate a markup file from image J

PostPosted: Sat Dec 13, 2014 5:53 pm
by edrosten
cedric wrote:Hey there,
- What is the role of this markup file?


3B is compuationally expensive, so it's necessary to run it on a limited area. The markup indicaes which area you want the analysis performed on.


- Could anyone know how to generate a markup file with image J?



For the plugin, you just need to select an area with the selection tools. The ellipse tool is a good one.

To convert the selection to a markup file, do:

Edit > Selection > Create Mask
Edit > Invert

Then the area you want should be in white and the rest in black. Save the resulting image and use it as markup.