This is a follow-up to my previous post here
I’ve followed the steps mentioned in the previous post.
- Loaded the z-stack image
- Downsampled the image by 4
- Could use the 3D viewer plugin to obtain the 3D reconstruction
Next, I’d like to use the local thickness plugin to retain segments of the 3D volume that has a thickness of 1 - 10 um.
From the suggestions given in my previous post, I tried to use the “Local thickness” plugin.
//Step 1: Generates Local Thickness images
run(“Local Thickness (complete process)”, “threshold=1”);
// Step 2: Threshold it
// Step 3: Convert to mask
run(“Convert to Mask”, “method=Default background=Dark black”);
Output obtained after step 1:
Next, I try to follow step 2 and 3 in Image -> Adjust -> Threshold
After I type 1.0 and 10.0 and hit Apply, 10.0 automatically changes to 1e30. I am not sure why this happens.
If I ignore the change (10.0 to 1e30 after hitting apply) and use the 2D slice obtained after local-thickness function, the following is obtained
The segments are broken unfortunately. I’m not sure why this happens
Any suggestions on how to proceed will be really helpful