Formerly known as Segmenter
Probability Map Viewer is a web application using an embedded Jetty web server that performs probability map generation in near real time on tiled image data. Probability Map Viewer is designed to be run on a linux machine with the web application viewable locally or remotely via a web browser.
Probability map generation can be performed by an external command line script.
Publication
Churas,C. et al. (2017) Probability Map Viewer: near real-time probability map generator of serial block electron microscopy collections. Bioinformatics, 33, 3145–3147.
Probability Map Viewer supports two modes, a single image analysis mode and collection mode. In collection mode Probability Map Viewer automatically switches to the latest image that appears in a user specified directory.
- Centos 6+, Ubuntu 12+, and most other linux distributions should work
- Java 8+ (jdk to build)
- Image Magick command line programs (namely convert)
- Matlab Runtime 2013a (needed to run CHM)
- chmutil (used when probabilitymapviewer is converting dm4 files via --dm4collectionmode)
- IMOD (used to convert dm4 files via --dm4collectionmode)
A pre-built jar is available here: https://github.com/crbs/probabilitymapviewer/releases
Probability Map Viewer is started via the command line.
For usage instructions run the following command (assuming the jar file is in the current working directory):
java -jar probabilitymapviewer-3.0.1-jar-with-dependencies.jar -hOR
Click launch button below to spin up latest release of Probability Map Viewer on the cloud (~10 minute spin up time): (Oregon region)
Click here for detailed instructions on launching Probability Map Viewer via AWS CloudFormation
For more information visit the wiki:
Probability Map Viewer build requirements:
Commands build Probability Map Viewer assuming machine has Git command line tools installed:
# In lieu of git one can just download repo and unzip it
git clone https://github.com/crbs/probabilitymapviewer.git
cd probabilitymapviewer
mvn clean test installThe above command will create a jar file under target/ named probabilitymapviewer-<VERSION>-jar-with-dependencies.jar
Copyright 2016 The Regents of the University of California All Rights Reserved
Permission to copy, modify and distribute any part of this Probability Map Viewer 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 Probability Map Viewer 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:invent@ucsd.edu.
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 Probability Map Viewer, EVEN IF THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
THE Probability Map Viewer 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 Probability Map Viewer WILL NOT INFRINGE ANY PATENT, TRADEMARK OR OTHER RIGHTS.
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Support from NIH grants 5P41GM103412 (NCMIR) and 5P41GM103426 (NBCR).
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This research benefitted from the use of credits from the National Institutes of Health (NIH) Cloud Credits Model Pilot, a component of the NIH Big Data to Knowledge (BD2K) program.