{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,29]],"date-time":"2026-03-29T11:05:03Z","timestamp":1774782303291,"version":"3.50.1"},"reference-count":65,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2015,3,9]],"date-time":"2015-03-09T00:00:00Z","timestamp":1425859200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Computation"],"abstract":"<jats:p>In this review, we describe computational features of computer-assisted microscopy that are unique to the Center for Microbial Ecology Image Analysis System (CMEIAS) software, and examples illustrating how they can be used to gain ecophysiological insights into microbial adaptations occurring at micrometer spatial scales directly relevant to individual cells occupying their ecological niches in situ. These features include algorithms that accurately measure (1) microbial cell length relevant to avoidance of protozoan bacteriovory; (2) microbial biovolume body mass relevant to allometric scaling and local apportionment of growth-supporting nutrient resources; (3) pattern recognition rules for morphotype classification of diverse microbial communities relevant to their enhanced fitness for success in the particular habitat; (4) spatial patterns of coaggregation that reveal the local intensity of cooperative vs. competitive adaptations in colonization behavior relevant to microbial biofilm ecology; and (5) object segmentation of complex color images to differentiate target microbes reporting successful cell-cell communication. These unique computational features contribute to the CMEIAS mission of developing accurate and freely accessible tools of image bioinformatics that strengthen microscopy-based approaches for understanding microbial ecology at single-cell resolution.<\/jats:p>","DOI":"10.3390\/computation3010072","type":"journal-article","created":{"date-parts":[[2015,3,9]],"date-time":"2015-03-09T11:47:19Z","timestamp":1425901639000},"page":"72-98","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":23,"title":["Use of CMEIAS Image Analysis Software to Accurately Compute Attributes of Cell Size, Morphology, Spatial Aggregation and Color Segmentation that Signify in Situ Ecophysiological Adaptations in Microbial Biofilm Communities"],"prefix":"10.3390","volume":"3","author":[{"given":"Frank","family":"Dazzo","sequence":"first","affiliation":[{"name":"Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA"}]},{"given":"Brighid","family":"Niccum","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA"}]}],"member":"1968","published-online":{"date-parts":[[2015,3,9]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1007\/s002480000004","article-title":"CMEIAS: A computer-aided system for the image analysis of bacterial morphotypes in microbial communities","volume":"41","author":"Liu","year":"2001","journal-title":"Microb. Ecol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1111\/j.1462-2920.2005.00880.x","article-title":"Daime, a novel image analysis program for microbial ecology and biofilm research","volume":"8","author":"Daims","year":"2006","journal-title":"Environ. Microbiol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1007\/s00253-007-0886-z","article-title":"Quantification of uncultured microorganisms by fluorescence microscopy and digital image analysis","volume":"75","author":"Daims","year":"2007","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"426","DOI":"10.3390\/d5030426","article-title":"In situ ecophysiology of microbial biofilm communities analyzed by CMEIAS computer-assisted microscopy at single-cell resolution","volume":"5","author":"Dazzo","year":"2013","journal-title":"Diversity"},{"key":"ref_5","unstructured":"CMEIAS Center for Microbial Ecology Image Analysis System Project Website. Available online: http:\/\/cme.msu.edu\/cmeias\/."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Guerrero, R., and Pedros-Alio, C. (1993). Trends in Microbial Ecology, Spanish Society for Microbiology.","DOI":"10.1007\/978-1-4615-2858-6_4"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1111\/j.1365-2818.1993.tb03371.x","article-title":"Direct identification and localization of Azospirillum in the rhizosphere of wheat using fluorescence-labeled monoclonal antibodies and confocal scanning laser microscopy","volume":"171","author":"Schloter","year":"1993","journal-title":"J. Microsc."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1013","DOI":"10.1128\/aem.61.3.1013-1019.1995","article-title":"In situ localization of Azospirillum brasilense in the rhizosphere of wheat with fluorescently labeled, rRNA-targeted oligonucleotide probes and scanning confocal laser microscopy","volume":"61","author":"Assmus","year":"1995","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"7271","DOI":"10.1128\/AEM.71.11.7271-7278.2005","article-title":"Ascending migration of endophytic rhizobia, from roots to leaves, inside rice plants and assessment of benefits to rice growth physiology","volume":"71","author":"Chi","year":"2005","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Hurst, C.J., Crawford, R.L., Garland, J., Lipson, D., Mills, A., and Stetzenback, L.J. (2007). Manual of Environmental Microbiology, American Society for Microbiology Press. [3rd ed.].","DOI":"10.1128\/9781555815882"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Lewandowski, Z., and Beyenal, H. (2007). Fundamentals of Biofilm Research, CRC.","DOI":"10.1201\/b15996"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1128\/aem.42.1.142-149.1981","article-title":"Microcomputer assisted biomass determination of planktonic bacteria on scanning electron micrographs","volume":"42","author":"Krambeck","year":"1981","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_13","unstructured":"Wilkinson, M.H.F., and Schut, F. (1998). Digital Image Analysis of Microbes: Imaging, Morphometry, Fluorometry and Motility Techniques and Applications, Wiley."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"2762","DOI":"10.1128\/aem.55.11.2762-2772.1989","article-title":"Evaluation of automated threshold selection methods for accurately sizing microscopic fluorescent cells by image analysis","volume":"55","author":"Sieracki","year":"1989","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"596","DOI":"10.1007\/s00248-014-0410-9","article-title":"Accuracy of biovolume formulas for CMEIAS computer-assisted microscopy and body size analysis of morphologically diverse microbial populations and communities","volume":"68","author":"Folland","year":"2013","journal-title":"Microb. Ecol."},{"key":"ref_16","unstructured":"Duda, R., and Hart, P. (1973). Pattern Classification and Scene Analysis, John Wiley & Sons."},{"key":"ref_17","first-page":"153","article-title":"Feature selection: Evaluation, application, and small sample performance","volume":"19","author":"Jain","year":"1993","journal-title":"Inst. Electr. Electron. Eng. Trans. Pattern Anal. Mach. Intell."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1383","DOI":"10.1016\/0031-3203(93)90144-L","article-title":"Extracting natural scales using Fourier descriptors","volume":"26","author":"Rosin","year":"1993","journal-title":"Pattern Recognit."},{"key":"ref_19","first-page":"1","article-title":"A consistent attributed graph-based hand-drawn circuit diagram reading system","volume":"4","author":"Yu","year":"1995","journal-title":"Chin. J. Electron."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"744","DOI":"10.2307\/1938482","article-title":"Geostatistics in ecology: Interpolating with known variance","volume":"68","author":"Robertson","year":"1987","journal-title":"Ecology"},{"key":"ref_21","first-page":"147","article-title":"Quantitative indices for the autecological biogeography of a Rhizobium endophyte of rice at macro and micro spatial scales","volume":"35","author":"Dazzo","year":"2003","journal-title":"Symbiosis"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"7047","DOI":"10.3390\/s120607047","article-title":"CMEIAS-aided microscopy of the spatial ecology of individual bacterial interactions involving cell-to-cell communication within biofilms","volume":"12","author":"Dazzo","year":"2012","journal-title":"Sensors"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1007\/s00248-009-9616-7","article-title":"CMEIAS color segmentation: An improved computing technology to process color images for quantitative microbial ecology studies at single-cell resolution","volume":"59","author":"Gross","year":"2010","journal-title":"Microb. Ecol."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Wiesmann, V., Franz, D., Held, C., Munzenmayer, C., Palmisano, R., and Wittenberg, T. (2014). Review of free software tools for image analysis of fluorescence cell micrographs. J. Microsc., 257.","DOI":"10.1111\/jmi.12184"},{"key":"ref_25","unstructured":"Dazzo, F.B., Liu, J., Gross, C., Reddy, C., Monosmith, C., Philips, N., Radek, C., Klemmer, K.J., Ji, Z., and Smith, P. CMEIAS v3.10: Advanced computational tools of image analysis software designed to strengthen microscopy-based approaches for understanding microbial ecology. Available online:http:\/\/lter.kbs.msu.edu\/abstracts\/434."},{"key":"ref_26","unstructured":"Roberts, A., and Withers, P. (2012). StatistiXL, Version 1.10, Broadway-Nedlands."},{"key":"ref_27","first-page":"1","article-title":"PAST: Paleontological statistics software package for education and data analysis","volume":"4","author":"Hammer","year":"2001","journal-title":"Palaeontol. Electron."},{"key":"ref_28","unstructured":"Towner, H. (1999). EcoStat, Version 1.03, Trinity Software Inc."},{"key":"ref_29","unstructured":"(2004). GS+, Version 7.0., Gamma Design Software."},{"key":"ref_30","unstructured":"Magurran, A.E. (2004). Measuring Biological Diversity, Blackwell Publishing."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"4050","DOI":"10.1128\/AEM.66.9.4050-4057.2000","article-title":"Parallel processing of substrate correlates with greater functional stability in methanogenic bioreactor communities perturbed by glucose","volume":"66","author":"Hashsham","year":"2000","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"4058","DOI":"10.1128\/AEM.66.9.4058-4067.2000","article-title":"Flexible community structure correlates with stable community function in methanogenic bioreactor communities perturbed by glucose","volume":"66","author":"Fernandez","year":"2000","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Ritchie, M.E. (2010). Scale, Heterogeneity, and the Structure and Diversity of Ecological Communities, Princeton University Press.","DOI":"10.1515\/9781400831685"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1086\/523950","article-title":"Optimal cell size for resource uptake in fluids: A new facet of resource competition","volume":"171","author":"Yoshiyama","year":"2008","journal-title":"Am. Nat."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1080\/00222938300770671","article-title":"The detection of differences among assemblages of marine benthic species based on an assessment of dominance and diversity","volume":"17","author":"Lambshead","year":"1983","journal-title":"J. Nat. Hist."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Gaston, K.J. (1994). Rarity, Springer.","DOI":"10.1007\/978-94-011-0701-3"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"2473","DOI":"10.1073\/pnas.012579799","article-title":"Allometric scaling of metabolic rate from molecules and mitochondria to cells and mammals","volume":"99","author":"West","year":"2002","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"930","DOI":"10.1128\/aem.46.4.930-940.1983","article-title":"Effects of nutrient deprivation on Vibrio cholerae","volume":"46","author":"Baker","year":"1983","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1111\/j.1574-6941.1993.tb00034.x","article-title":"Changes in viability, respiratory activity, and morphology of the marine Vibrio sp. strain S14 during starvation of individual nutrients and subsequent recovery","volume":"12","author":"Holmquist","year":"1993","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"191","DOI":"10.2307\/5493","article-title":"A simple test for change in community structure","volume":"2","author":"Solow","year":"1993","journal-title":"J. Anim. Ecol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1300","DOI":"10.1126\/science.277.5330.1300","article-title":"The influence of functional diversity and composition on ecosystem processes","volume":"277","author":"Tilman","year":"1997","journal-title":"Science"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"2247","DOI":"10.1111\/j.1462-2920.2012.02817.x","article-title":"Culturing captures members of the soil rare biosphere","volume":"14","author":"Shade","year":"2012","journal-title":"Environ. Microbiol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"2415","DOI":"10.1890\/06-0937.1","article-title":"Predator diversity and trophic interactions","volume":"88","author":"Schmitz","year":"2007","journal-title":"Ecology"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"131","DOI":"10.3354\/ame012131","article-title":"Impact of metazoan and protozoan grazers on bacterial biomass distribution in microcosm experiments","volume":"12","author":"Arndt","year":"1997","journal-title":"Aquat. Microb. Ecol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1128\/AEM.65.1.25-35.1999","article-title":"Bacterial filament formation, a defense mechanism against flagellate grazing, is growth rate controlled in bacteria of different phyla","volume":"65","author":"Hahn","year":"1999","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1128\/aem.56.3.583-589.1990","article-title":"Size-selective grazing on bacteria by natural assemblages of estuarine flagellates and ciliates","volume":"56","author":"Gonzalez","year":"1990","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Hildrew, A., Raffelli, D., and Edmonds-Brown, R. (2007). Body Size: The Structure and Function of Aquatic Ecosystems, Cambridge University Press.","DOI":"10.1017\/CBO9780511611223"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"1771","DOI":"10.1890\/03-9000","article-title":"Toward a metabolic theory of ecology","volume":"45","author":"Brown","year":"2004","journal-title":"Ecology"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1146\/annurev.es.20.110189.001131","article-title":"Landscape ecology: The effect of pattern on process","volume":"20","author":"Turner","year":"1989","journal-title":"Annu. Rev. Ecol. Syst."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"693","DOI":"10.2307\/3133","article-title":"Stability in insect host-parasite models","volume":"42","author":"Hassell","year":"1973","journal-title":"J. Anim. Ecol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1008","DOI":"10.1890\/0012-9658(1998)079[1008:MOSPFC]2.0.CO;2","article-title":"Measures of spatial patterns for counts","volume":"79","author":"Perry","year":"1998","journal-title":"Ecology"},{"key":"ref_52","unstructured":"Mendez-Vilas, A., and Diaz, J. (2010). Microscopy: Science, Technology, Applications and Education, Formatex Res Center."},{"key":"ref_53","first-page":"845","article-title":"The beneficial plant growth-promoting association of Rhizobium leguminosarum bv. trifolii with rice roots","volume":"28","author":"Yanni","year":"2001","journal-title":"Aust. J. Plant Physiol."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Varma, A., Abbott, L., Werner, D., and Hampp, R. (2004). Plant Surface Microbiology, Springer-Verlag.","DOI":"10.1007\/978-3-540-74051-3"},{"key":"ref_55","unstructured":"Garland, J., Hurst, C., Lipson, D., Mills, A., Stetzenbach, L., and Crawford, R. (2007). Manual of Environmental Microbiology, American Society for Microbiology Press. [3rd ed.]. Chapter 59."},{"key":"ref_56","first-page":"733","article-title":"CMEIAS: An improved computing technology for quantitative image analysis of root colonization by rhizobacteria in situ at single-cell resolution","volume":"Volume 2","author":"DeBruijn","year":"2013","journal-title":"Molecular Microbial Ecology of the Rhizosphere"},{"key":"ref_57","unstructured":"Schmidt, T., and Schaechter, M. (2012). Topics in Ecological and Environmental Microbiology, Elsevier Press."},{"key":"ref_58","unstructured":"Singh, D.P., and Singh, H. (2014). Trends in Soil Ecology, Studium Press."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00248-006-9114-0","article-title":"Assessing primary and bacterial production rates in biofilms on pebbles in Ishite Stream, Japan","volume":"52","author":"Fukuda","year":"2006","journal-title":"Microb. Ecol."},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Ji, Z., Card, K., and Dazzo, F.B. (2014). CMEIAS JFrad: A new computing toolkit to discriminate the fractal geometry of landscape architecture and spatial patterns of individual cells in microbial biofilms. Microb. Ecol.","DOI":"10.1007\/s00248-014-0495-1"},{"key":"ref_61","first-page":"1","article-title":"CMEIAS Quadrat Maker: A digital software tool to optimize grid dimensions and produce quadrat images for landscape ecology spatial analysis","volume":"3","author":"Dazzo","year":"2013","journal-title":"J. Ecosyst. Ecogr."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"261","DOI":"10.2307\/2257973","article-title":"Some new tests of randomness","volume":"53","author":"Holgate","year":"1965","journal-title":"J. Ecol."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1111\/j.2517-6161.1979.tb01091.x","article-title":"Tests of \u201crandomness\u201d for spatial point patterns","volume":"41","author":"Ripley","year":"1979","journal-title":"J. R. Stat. Soc."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1016\/S0169-5347(02)02496-5","article-title":"Spatial soil ecology","volume":"17","author":"Ettema","year":"2002","journal-title":"Trends Ecol. Evol."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1111\/j.1574-6941.2005.00037.x","article-title":"In situ spatial scale of calling distances and population density-independent N-acylhomoserine lactone mediated communication by rhizobacteria colonized on plant roots","volume":"56","author":"Gantner","year":"2006","journal-title":"FEMS Microb. Ecol."}],"container-title":["Computation"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-3197\/3\/1\/72\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T20:43:16Z","timestamp":1760215396000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-3197\/3\/1\/72"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,3,9]]},"references-count":65,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2015,3]]}},"alternative-id":["computation3010072"],"URL":"https:\/\/doi.org\/10.3390\/computation3010072","relation":{},"ISSN":["2079-3197"],"issn-type":[{"value":"2079-3197","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,3,9]]}}}