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Bioinformatics. 2017 Oct 1;33(19):3145-3147. doi: 10.1093/bioinformatics/btx376.

Probability Map Viewer: near real-time probability map generator of serial block electron microscopy collections.

Author information

1
National Center for Microscopy and Imaging Research (NCMIR).
2
National Biomedical Computation Resource (NBCR).
3
Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA.

Abstract

Summary:

To expedite the review of semi-automated probability maps of organelles and other features from 3D electron microscopy data we have developed Probability Map Viewer, a Java-based web application that enables the computation and visualization of probability map generation results in near real-time as the data are being collected from the microscope. Probability Map Viewer allows the user to select one or more voxel classifiers, apply them on a sub-region of an active collection, and visualize the results as overlays on the raw data via any web browser using a personal computer or mobile device. Thus, Probability Map Viewer accelerates and informs the image analysis workflow by providing a tool for experimenting with and optimizing dataset-specific segmentation strategies during imaging.

Availability and implementation:

https://github.com/crbs/probabilitymapviewer.

Contact:

mellisman@ucsd.edu.

Supplementary information:

Supplementary data are available at Bioinformatics online.

PMID:
28957496
PMCID:
PMC5870650
DOI:
10.1093/bioinformatics/btx376
[Indexed for MEDLINE]
Free PMC Article

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