Performs automated point counting stereology on greyscale probability maps.
A probability map is simply an image with pixel values of 0-255 where the higher the value the more likely a given pixel belongs to whatever feature being segmented.
# download stereopointcounter
wget https://github.com/slash-segmentation/stereopointcounter/archive/master.zip
unzip master.zip
mkdir stereo_build
cd stereo_build
cmake ../stereopointcounter-master
make
stereopointcounter
usage: stereopointcounter [options]
Performs automated stereology point counting on probability map images passed in
via --images path.
This tool looks for *.png files and assumes they are 8-bit greyscale images all
with the same size.
Output is to standard out and format is comma separated variables in the
following format:
Image,GridSize,GridSizePixel,Positive,Total
/../foo.png,12x8,120x80,10,,67
...
...
Seconds,GrandTotalPositive,GrandTotal
123,29342,234292
Options:
--help, -h Print usage and exit.
--version, -v Print version and exit.
--images, -m Can be set to a single greyscale 8-bit image or directory of
8-bit greyscale *.png images
--gridx, Grid size in X. A value of say 4 means to generate
4vertical lines evenly spaced across the image.
--gridy, Grid size in Y. A value of say 8 means to generate
8horizontal lines evenly spaced across the image.
--threshold, -t Threshold to for pixel intensity that denotes a given pixel
intersection is a positive hit (0 - 255)
--saveimages, -s If set to <dir>, writes out images as RGB with grid
overlayed in red and green circles denoting intersections
with matches to a file with format of
grid(--gridx)x(--gridy)_pixel(pixelw)x(pixelh)_thresh(-t).(o
rigname)
Here is the output image from stereopointcounter with --saveimages flag turned on:
stereopointcounter --images probmap.png --gridx 52 --gridy 50 --threshold 200 --saveimages .
Output to standard out
This is the output from running the above command. --images can be given a single png file or a directory containing a set of png files.
Image,GridSize,GridSizePixel,Positive,Total
probmap.png,52x50,23x16,111,2548
Seconds,GrandTotalPositive,GrandTotal
0.22234,111,2548
The above output is in csv format and breaks down number of intersections where the pixel value at the intersection meets or exceeds the threshold set by --threshold flag. At the very end of the output is a summary denoting totals for all png images analyzed.
Image written to directory specified by --saveimages
Each intersection is examined and those intersections above the threshold which in the example case is 200 is circled in green and counted in the stats displayed above.
Copyright 2015 The Regents of the University of California All Rights Reserved
Permission to copy, modify and distribute any part of this stereopointcounter for educational, research and non-profit purposes, without fee, and without a written agreement is hereby granted, provided that the above copyright notice, this paragraph and the following three paragraphs appear in all copies.
Those desiring to incorporate this stereopointcounter into commercial products or use for commercial purposes should contact the Technology Transfer Office, University of California, San Diego, 9500 Gilman Drive, Mail Code 0910, La Jolla, CA 92093-0910, Ph: (858) 534-5815, FAX: (858) 534-7345, E-MAIL:[email protected].
IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS stereopointcounter, EVEN IF THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
THE stereopointcounter PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE UNIVERSITY OF CALIFORNIA HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS. THE UNIVERSITY OF CALIFORNIA MAKES NO REPRESENTATIONS AND EXTENDS NO WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR THAT THE USE OF THE stereopointcounter WILL NOT INFRINGE ANY PATENT, TRADEMARK OR OTHER RIGHTS.