Problem using 3D hysteresis

Usage & Issues
#1

Hi all,
I just used 3D hysteresis thresholding of the 3D ImageJ suite as normal - so I thought - but it now only returned a 2D image instead of an 3D stack. I ran:

run(“3D Hysteresis Thresholding”, “high=128 low=50”);

Am I missing some recent changes?
Best,
Maik

#2

Hi @Maik-Lu,

Please check that your stack is a Z-stack not a time-series. In case you have T instead of Z for the third dimension, you can swap the values in Image/Properties.

Hope this helps,

Best

Thomas

1 Like
#3

Hi @ThomasBoudier
thank you for your fast reply. Indeed I didn’t recognized, that during tubeness filter the slices merged into channels. I used the following jython code.
Thank you for this note, no I can go on :).

#@ Integer sigma1
#@OUTPUT Dataset output
#@ OpService ops
#@ DatasetService ds
#@ ConvertService convertService
from net.imagej import Dataset
from ij import WindowManager as wm

img = wm.getCurrentImage()	
data = convertService.convert(img, Dataset)
tube = ops.filter().tubeness(data,sigma1)
# Create output Dataset
output = ds.create(tube)