Creating a mask. CT scans



Hi everyone,
I just started my adventure with ImageJ. I was trying to invent something for my own, but I did not succeed. My job is the following.

I have CT scans of anthropomorphic phantom (chest, stomach: lungs, liver, heart, breast). Each element in the CT test was filled with salt solution of different concentration, so each of them had a different HU value (gray value). Images are sequences (.tiff). How can I create a mask for each element? In an easy way…
I need each organ separately for further analysis.

I will be very grateful for the help and explanation step by step


Hello @marinaanna and welcome to the ImageJ forum!

Can you post any of your images here so we better understand your problem? Thanks!


For example:

breast, inside: lungs, top of a liver and heart:


lungs. heart:


I was trying to select a region that I was interested in (for example: liver) - using a wand tool (increased the tolerance). I did it for a number of slices and used a “Interpolate” option in ROI Manager to do this for all slices (for liver it was about 300 images). I filled this areas with blue color and I wanted to create a mask… but it works only for one picture - I have over 300. It must be better way than doing it manually

How can I make masks for every slice I select in ROI Manager (for a whole sequence of images)? And get as a result the masks in the sequence?


Have you tried converting your image to 8-bit (right now it is RGB) and use something like the Morphological Segmentation plugin?


I did something like that:

  1. Add ROIs in ROI Manager (used wand tool and Interpolate ROIs option)
  2. Fill every of ROIs with color
  3. Save as a
  4. Open a new Image (same number of slice)
  5. Use: Image >> Overlay >> From ROI Manager
  6. and: Process >> Binary >> Conver to Mask (as a .tif)

I received what I wanted, but …I did not use the information that every single organ is a different value (don’t know how to use Threshold to do this…) I think I do it manually instead of using the HU value.

Can I ask you about Morphological Segmentation plugin? Sorry for such trivial questions. I’ve got Fiji version and I really don’t know how can I get this plugin.

Thank you for your answer!


Sorry for the late answer. You can get the plugin by activating the IJPB-plugins update site. Follow the instructions in the plugin wiki page and let me know if you don’t manage to install it.