"stereo": a computer program for simulating stereologic volumetry of 3D discrete images using either random or fixed test grid placement across slices.
http://www.nil.wustl.edu/labs/kevin/stereo.htm
or http://purl.org/net/kbmd/stereo
Downloading the program.
System requirements: This is compiled and tested for SunOS 4.1.3 on a Sparc10. The source code is not publicly available.
Running "stereo": Type the command without other parameters. The image needs to be in ANALYZE 8-bit image format, including a valid .hdr file. The program considers all voxels with value > 0 to be part of the structure of interest, while all voxels with value 0 are ignored. Running stereo for the images listed below with 100,000 trials took between a few minutes and 6 hours on the system described above, so running it in batch mode is wise. It is wise to redirect the standard output since it is voluminous, e.g. "stereo [parameters] > output.txt". The resulting text file can be viewed or printed, but the key elements needed for statistical analysis are marked by a "#" symbol. This allows e.g. "grep # output.txt > info.txt" to extract the most important information from the file. The actual volume of the structure of interest (in voxels) is computed and reported at the top of the output file and can be viewed by typing e.g. "head -10 output.txt". The "info.txt" file is space- and LF- delimited and can be easily imported into Excel.
Download stereo, "test" C shell script, and the test images described in the above paper (*.hdr, *.img).