3D imaging of microbial biofilms: Integration of synchrotron imaging and an interactive visualization interface
Understanding the structure of microbial biofilms and other complex microbial communities is now possible through x-ray microtomography imaging. Feature detection and image processing for this type of data focuses on efficiently identifying and segmenting biofilm biomass in the datasets. These datas...
Saved in:
Published in | 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society Vol. 2014; pp. 3304 - 3307 |
---|---|
Main Authors | , , , , , |
Format | Conference Proceeding Journal Article |
Language | English |
Published |
United States
IEEE
01.01.2014
|
Subjects | |
Online Access | Get full text |
Cover
Loading…
Summary: | Understanding the structure of microbial biofilms and other complex microbial communities is now possible through x-ray microtomography imaging. Feature detection and image processing for this type of data focuses on efficiently identifying and segmenting biofilm biomass in the datasets. These datasets are very large and segmentation often requires manual interventions due to low contrast between objects and high noise levels. New software is required for the effectual interpretation and analysis of such data. This work specifies the evolution and ability to analyze and visualize high resolution x-ray microtomography datasets. Major functionalities include read/write with multiple popular file formats, down-sampling large datasets to generate quick-views on low-power computers, image processing, and generating high quality output images and videos. These capabilities have been wrapped into a new interactive software toolkit, BiofilmViewer. A major focus of our work is to facilitate data transfer and to utilize the capabilities of existing powerful visualization and analytical tools including MATLAB, ImageJ, Paraview, Chimera, Vaa3D, Cell Profiler, Icy, BioImageXD, and Drishti. |
---|---|
ISSN: | 1094-687X 1557-170X 1558-4615 |
DOI: | 10.1109/EMBC.2014.6944329 |