Author:
Pasulka Alexis L.,Hood Jonathan F.,Michels Dana E.,Wright Mason D.
Abstract
AbstractEpifluorescence microscopy is an essential tool for obtaining reliable estimates of the abundance of marine microorganisms including viruses. However, computational analysis is required to gain consistent and quantitative data from digital microscopy images. Many imaging programs are proprietary and cost-prohibitive. The currently available free imaging programs are often platform specific and/or lack the flexibility to analyze microscopy images from natural samples, such as the planktonic environment, which can contain challenges such as debris and high background signals. Here we describe two MATLAB-based open-source image analysis programs that work across computer platforms and provide the tools to analyze a range of image types and cell sizes with a user-friendly interface. The Microbial Image Analysis (MiA) program aims to provide flexibility for the selection, identification, and quantification of cells that vary in size and fluorescence intensity within natural microbial communities. The Viral Image Analysis (ViA) program aims to provide an effective means for quantifying viral abundances from epifluorescence images as well as enumerating the intensity of a primary and secondary stain. In this paper, we provide an overview of the functionality of the MiA and ViA programs and highlight specific program features through several microbial image case studies.
Publisher
Cold Spring Harbor Laboratory
Reference46 articles.
1. Single‐cell and population level viral infection dynamics revealed by phage
FISH
, a method to visualize intracellular and free viruses
2. Barrero-Canosa, J. and Moraru, C. (2018). PhageFISH for monitoring phage infections at single cell level. In Martha R. J. Clokie et al. (eds.), Bacteriophages: Methods and Protocols, Volume IV, Methods in Molecular Biology, vol. 1898.
3. RAPID: research on automated plankton identification;Oceanography,2007
4. CellProfiler: image analysis software for identifying and quantifying cell phenotypes;Genome Biology,2006
5. Technique for the enumeration of heterotrophic and phototrophic nanoplankton, using epi-fluorescence microscopy, and comparison with other procedures;Appl. Environ. Microbiol,1983