This plugin Counts the thresholded voxels in a stack and displays
the count, the average count per slice and the volume fraction (ratio of thresholded voxels to all voxels).
If there is an ROI, the voxel counts and volume fraction are based on the substack defined by that ROI.
Before running, threshold the stack using Image/Adjust/Threshold.
With binary stacks, black voxels are assummed to be thresholded.
The following summary information is provided:
Thresholded voxels – count of thresolded voxels inside ROI
Average voxels per slice – average number of thresolded voxels per slice
Total ROI voxels – count of all voxels within ROI
Volume fraction – 100*(Thresolded voxels)/(Total ROI voxels)
Voxels in stack – number of voxels in stack. With no ROI, this
is the same as “Total ROI voxels”.
Additional information is provided if the stack is spatially calibrated:
Voxel size – the width, height and depth of a single voxel,
as defined in the Image>Properties dialog box
Average volume per slice – average voxels per slice * voxel size
Total ROI volume – total ROI voxels * voxel size
Volume of stack – voxels in stack * voxel size
Note that the Analyze>Histogram command
also counts thresholded voxels when “Limit to Threshold” is checked
in Analyze>Set Measurements.
2002/01/11: First vesion
2002/01/28: Works with binary stacks
2002/08/19: Volume fraction based on ROI
2006/05/11: Measures volume in real-world units (e.g., mm^3)
2010/04/27: Works with stacks larger than 2 gigapixels
Author: Joachim Walter (walter at biz.uni-muenchen.de) History: 2003/11/24: First version 2003/12/20: Adds “Scale:” option; macro recording works 2005/06/17: Improved and built into Image5D Source: Hypervolume_Opener.java
Author: Jeffrey Kuhn (firstname.lastname@example.org) The University of Texas at Austin Date: 2001/2/14 Source: Click_Forward_.java Installation: Copy Click_Forward_.class to the plugins folder and restart ImageJ. Description:
Authors: Patrick Pirrotte & Jerome Mutterer (jerome.mutterer at ibmp-ulp.u-strasbg.fr) Jeff Brandenburg, Duke Center for In-Vivo Microscopy (jeffb at orion.duhs.duke.edu) History: 2003/03/28: First version 2005/08/15: Added