Determining Area Loss (% Area) - FIJI - BigWarp

I’ve used the BigWarp plugin on FIJI in order to align 2 images of tissue, before and after being subjected to damage. I would like to examine the % tissue area that is lost from the before image in the after image after the composite has been generated in BigWarp.

I have nice looking BigWarp composites, but can’t figure out how to determine the area lost in the after image with reference to the before image (tissue 1 vs. tissue 2, not just tissue 1+2 vs. background). I have tried selecting the area with a tool and Analyze --> Measure but this seems to only give me the % Area of the signal from the tissue vs. the blank space.

Any help would be greatly appreciated!

Hi @cel,

Welcome to the forum.

It it right that you’re able to measure the area of (tissue 1) and (tissue 2 post warp) individually?
If that’s right, is what you want to have a program compute the ratio of those areas?

If I’m misunderstanding, you can attach images to this forum post which may help us understand your goal.


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Thank you for your quick reply,

Since it’s the same tissue before and after, it would be necessary to determine the ratio of the 2 areas (area loss). I could calculate the areas for the two images (image 1 and image 2 post warp) independently using the measuring tool by tracing around the area of the tissue with the freehand selection tool, then comparing the results. However, manually tracing 2 separate times can introduce variability. Ideally it would be possible to determine the area loss in 1 step by simply doing something with the Bigwarp image as it overlays the before and after images.

Also, we have particular regions of interest in the tissue. We thought that using Bigwarp to overlay the images could allow us to look at tissue loss in specific ROIs. However, I believe that the measurement tool compares signal / no signal and not differences among 2 channels.

In general, I’m just looking to find a way to find differences in area between the before and after images in a simple way that is going to be methodically sound enough to hold up in a publication.

If there’s any way to do this that I’m missing, please let me know! Thank you very much for your help.

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Hi @cel,

I got it now, thanks for that detailed explanation.

If your images are 2d, you can warp your roi using the instructions on the bigwarp wiki page. If your images are 3d, then something is still possible, but more complicated - let me know if that is the case.

Assuming for now you have 2d images, and that you outlined the tissue you are interested in with some kind of ROI on the tissue 2 image (pre-warping).

Here’s something you could do:

  1. Install a bigwarp script that warps rois (see below).
  2. Use the new command to warp the roi into the tissue 1 image (see link above for more detailed instructions on hows this works).
  3. Measure the ROI size after warping.

The same kind of thing is possible if you drew the roi on the tissue 1 image, you just have to tell the algorithm which one it is.

I think that does just what you need, but definitely let me know if I missed something. Please post back if something is unclear, not working, or working perfectly.

Good luck,

On installing the script

Download this script, and put it in a subfolder of (I used Then a new option should appear in your Fiji menu (you’ll have to restart fiji if it’s open already).