Auto Selecting area


Is there anyway of using fiji to auto select around membranes instead of drawing around them with the freehand selections? Basically I would like to select the area shown in the image automatically (rather than with the freehand tool since its a little inaccurate). Once selected I’d like to clear the outside of the selected area.

Any help is appreciated, Thanks!

Have you tried an analyze particles step?
Also are you sure you don’t mean inside of the selection, clearing the whitespace? Or do you really want to get rid of the tissue?

Either way, to generate an approximate ROI using your modified image, I set it to 8bit, Smoothed it twice, and then used Analyze Particles with the settings shown.

Other posts should be able to help you transfer the annotation back into the original image if you need help with that step. Here I used Add[t] in the ROI Manager to manually add the automatically generated ROI.

Alternatively, if you want some manual control, you can right click on the Wand Tool and use that with a particular Tolerance. Here I chose 22.

And here recoloring the wand tool selection as Cyan.

1 Like