Final Protocol

Unvessel Protocols

Segmentation result

Left: Raw, Right: Segmented with threshold=0.8

Post-processing of segmentation results

1. With Fiji.app, load iba1_SEG_0pt80.

2. Process→Binary→Make Binary

   1. Method: Max Entropy

      

3. Process→Morphology→Gray Morphology

   1. Radius=2 (pixel), Method: dilate.

      

   Tubeness

   https://www.longair.net/edinburgh/imagej/tubeness/

   → doesn’t work

   #3

   • downsample in (x,y) by 0.4 x 0.4 → 410x410x1024

   • binarize with method triangle.

     

   • run tracing script

   • remove blood vessel with custom script

   • Subtract removed tif from traced tif

     • It’ll give a mask containing Blood Vessel only!

       

   • use binarize script to make [0, 255] to [0, 1]

   • Invert

     • Final MASK!

       

   • multiply final mask to the original image.

   Result on 0.41x downsampled stack

   

   Result on original image w/ rescaled back Mask