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CMEIAS Introduction

What is CMEIAS?

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Free image analysis software tools of bioimage informatics designed to strengthen microscopy-based approaches for understanding microbial ecology

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Custom DLL plug-ins for the host program UTHSCSA ImageTool operating in a PC with Windows 7 or 10 using the CMEIAS-IT ver. 1.28 Setup

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Interactive semi-automatic image editing and analysis of microbial abundance, luminosity and morphological diversity

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Object analysis and 1-D classification of microbial populations and communities using 34 different measurement features of object density, size, shape, location and luminance

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Supervised hierarchical classification of 11 different predominant microbial morphotypes by pattern recognition analysis of 8-bit grayscale digital images in various file formats

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Reports results on user-selected measurement attributes and on microbial morphotype diversity (richness and distribution of abundance) for all microbes found in the images in a grid format ready for export to a Windows-compatible spreadsheet program


The CMEIAS Color Segmentation program provides many digital tools to semi-automate the image editing tasks to segment the foreground objects of interest in complex color and grayscale images


The CMEIAS Quadrat Maker program provides the features to semi-automate the optimization of the grid lattice dimensions on landscape images and make the individual size-optimized quadrat images for plot-based spatial pattern analysis.


The CMEIAS JFrad program provides 11 computational methods to analyze the fractal dimensions of foreground object coastlines, e.g., biofilm landscapes that reflect microbial colonization behaviors optimized for resource apportionment and cell-cell interactions.


The CMEIAS Audio-Visual *.wmv files are available to demonstrate various features and protocols of CMEIAS software, including CMEIAS Color Segmentation, CMEIAS JFrad, and CMEIAS Quadrat Maker applications.


     CMEIAS Microscopy is one of the most important techniques in microbial ecology, since this is the most direct approach to examine the microbe's world from its own perspective, at spatial scales relevant to the microbes themselves. A major challenge in microbial ecology is to develop reliable and facile methods of computer-assisted microscopy that can analyze complex digital images of microbial populations and communities at single-cell resolution, and compute ecologically important quantitative phenotypic characteristics of their abundance, spatial organization, and diversity without cultivation. There are several advantages of using pattern recognition techniques in conjunction with computer-assisted microscopy and digital image analysis for quantitative studies of microbial communities. Automatic image analysis reduces the amount of tedious work with microscopes needed to accurately measure microbial abundance and their morphotype classification in situ. These techniques performed by CMEIAS provide a powerful quantitative phenotypic approach to analyze ecophysiological and spatial features that complement molecular microbial ecology approaches to analyze complex microbial communities in situ without cultivation.

     CMEIAS software is developed by a team of microbial ecologists, computer scientists and mathematicians at the MSU Center for Microbial Ecology. The core analytical program consists of several custom plug-ins that we have built for UTHSCSA ImageTool, a free image analysis software operating on a personal computer running 32- or 64-bit Windows operating system. The CMEIAS-IT Ver. 1.28 object analyzer extracts any user-selected combination of up to 34 measurement attributes (size, shape, luminosity and spatial coordinates) of each foreground object found in the image. The CMEIAS/IT 1-dimensional object classifier selectively groups objects within an image into up to 16 bins based on division of a scale defined by the upper class limits of a single measurement feature, in units defined by user-specified spatial calibration. The CMEIAS morphotype classifier automatically categorizes each foreground object in the image into one of 11 predominant microbial morphotypes, including cocci, spirals, curved rods, U-shaped rods, regular straight rods, unbranched filaments, ellipsoids, clubs, rods with extended prostheca, rudimentary branched rods, and branched filaments. The CMEIAS image analysis program and comprehensive testing results of its morphotype classification algorithms are described in detail in Liu et al. 2001.

     CMEIAS-IT Ver. 1.28 software is released as a free image analysis program that provides wide applications in microbial ecology research, training and education. A comprehensive operator manual plus interactive training tutorials providing background information and instructions to use this software are included with the CMEIAS-IT Ver. 1.28 program files available in the download area

A stand-alone CMEIAS Color Segmentation application toolkit is available to facilitate the image editing tasks required to segment and analyze foreground objects within complex images.

A stand-alone CMEIAS Quadrat Maker program is designed to help optimize the grid-lattice dimensions that divide landscape images into equal sized quadrats for plot-based spatial pattern analysis.

A Java-based CMEIAS JFrad program is designed to analyze the self-similar fractal dimensions of complex landscape architectures, e.g., microbial biofilms.

Several CMEIAS audio-visual *.wmv demos are available to introduce the main features of CMEIAS software, e.g., Color Segmentation, Quadrat Maker, and JFrad.

A major CMEIAS Image Analysis upgrade is currently under development and will be available at a future date. Periodically check the CMEIAS News page for update announcements. 

CMEIAS Editing feature

CMEIAS Color Segmentation Shield

CMEIAS Quadrat Maker Shield

CMEIAS JFrad Shield