Automated Counting of Bacterial Colony Forming Units on Agar Plates
Publication Date
March 20, 2012
Journal
PLOS ONE
Authors
Silvio D. Brugger, Christian Baumberger, Marcel Jost, Werner Jenni, et al
Volume
7
Issue
3
Pages
e33695
DOI
http://doi.org/10.1371/journal.pone.0033695
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0033695
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/22448267
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3308999
Europe PMC
http://europepmc.org/abstract/MED/22448267
Web of Science
000303855700058
Scopus
84858627076
Mendeley
http://www.mendeley.com/research/automated-counting-bacterial-colony-forming-units-agar-plates
Events
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Mendeley | Further Information

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CrossRef

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/665335"], "description"=>"<p>GUI showing a typical result obtained after counting a blood agar plate with pneumococcal colonies. Red: counted as a single bacterial colony. Green: counted as double colonies.</p>", "links"=>[], "tags"=>["interface", "automated"], "article_id"=>335824, "categories"=>["Information And Computing Sciences", "Chemistry", "Infectious Diseases"], "users"=>["Silvio D. Brugger", "Christian Baumberger", "Marcel Jost", "Werner Jenni", "Urs Brugger", "Kathrin Mühlemann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033695.g002", "stats"=>{"downloads"=>8, "page_views"=>75, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Graphical_user_interface_GUI_of_the_automated_colony_counter_/335824", "title"=>"Graphical user interface (GUI) of the automated colony counter.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-20 01:37:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/665480"], "description"=>"<p>Flowchart of the colony separation and counting algorithm.</p>", "links"=>[], "tags"=>["counting"], "article_id"=>335971, "categories"=>["Information And Computing Sciences", "Chemistry", "Infectious Diseases"], "users"=>["Silvio D. Brugger", "Christian Baumberger", "Marcel Jost", "Werner Jenni", "Urs Brugger", "Kathrin Mühlemann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033695.g004", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Flowchart_of_the_colony_separation_and_counting_algorithm_/335971", "title"=>"Flowchart of the colony separation and counting algorithm.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-20 01:39:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/665183"], "description"=>"<p>Hardware assembly of the automated colony counter.</p>", "links"=>[], "tags"=>["automated"], "article_id"=>335667, "categories"=>["Information And Computing Sciences", "Chemistry", "Infectious Diseases"], "users"=>["Silvio D. Brugger", "Christian Baumberger", "Marcel Jost", "Werner Jenni", "Urs Brugger", "Kathrin Mühlemann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033695.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hardware_assembly_of_the_automated_colony_counter_/335667", "title"=>"Hardware assembly of the automated colony counter.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-20 01:34:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/340977", "https://ndownloader.figshare.com/files/341048", "https://ndownloader.figshare.com/files/341116", "https://ndownloader.figshare.com/files/341183"], "description"=>"<div><p>Manual counting of bacterial colony forming units (CFUs) on agar plates is laborious and error-prone. We therefore implemented a colony counting system with a novel segmentation algorithm to discriminate bacterial colonies from blood and other agar plates.</p> <p>A colony counter hardware was designed and a novel segmentation algorithm was written in MATLAB. In brief, pre-processing with Top-Hat-filtering to obtain a uniform background was followed by the segmentation step, during which the colony images were extracted from the blood agar and individual colonies were separated. A Bayes classifier was then applied to count the final number of bacterial colonies as some of the colonies could still be concatenated to form larger groups.</p> <p>To assess accuracy and performance of the colony counter, we tested automated colony counting of different agar plates with known CFU numbers of <em>S. pneumoniae</em>, <em>P. aeruginosa</em> and <em>M. catarrhalis</em> and showed excellent performance.</p> </div>", "links"=>[], "tags"=>["automated", "counting", "bacterial", "forming", "units", "agar", "plates"], "article_id"=>127400, "categories"=>["Information And Computing Sciences", "Cancer", "Chemistry"], "users"=>["Silvio D. Brugger", "Christian Baumberger", "Marcel Jost", "Werner Jenni", "Urs Brugger", "Kathrin Mühlemann"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033695.s001", "https://dx.doi.org/10.1371/journal.pone.0033695.s002", "https://dx.doi.org/10.1371/journal.pone.0033695.s003", "https://dx.doi.org/10.1371/journal.pone.0033695.s004"], "stats"=>{"downloads"=>10, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Automated_Counting_of_Bacterial_Colony_Forming_Units_on_Agar_Plates/127400", "title"=>"Automated Counting of Bacterial Colony Forming Units on Agar Plates", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-03-20 02:03:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/665395"], "description"=>"<p>Blue channel of RGB images showing different colony morphologies of three different <i>S. pneumoniae</i> strains grown on blood agar plates.</p>", "links"=>[], "tags"=>["Infectious diseases", "computer science", "Gastroenterology and hepatology"], "article_id"=>335881, "categories"=>["Information And Computing Sciences", "Chemistry", "Infectious Diseases"], "users"=>["Silvio D. Brugger", "Christian Baumberger", "Marcel Jost", "Werner Jenni", "Urs Brugger", "Kathrin Mühlemann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033695.g003", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Colony_morphologies_/335881", "title"=>"Colony morphologies.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-20 01:38:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/665536"], "description"=>"<p><b>A.</b> Performance of automated colony counting (dots) of <i>S. pneumoniae</i> CFUs and routine manual counting (squares) versus the gold standard of manual counting on high performance images (X-axis). A total of 22 plates of 7 different pneumococcal strains were analyzed (CFU range 16–749; mean 133.5, median 55.5). Linear regression analysis of manual and automated colony count versus the gold standard showed a significant difference of the two slopes (p<0.0001) with a slope of 1.01(SD ±0.016; 95% confidence interval (CI) 0.98–1.04) for the automated colony counter and a slope of 0.67(SD±0.03; CI 0.61–0.73) for routine manual counting (95% confidence interval is indicated with dotted lines). <b>B.</b> Performance of automated colony counting (dots) of <i>S. pneumoniae</i> CFUs on blood agar plates versus the gold standard of manual counting on high performance images (X-axis). A total of 26 plates of 7 different pneumococcal strains (CFU range 36–853; mean 176, median 101.5) were analyzed. Linear regression showed a slope of 1.02 (SD±0.01; CI 1–1.03) (95% confidence interval is indicated with dotted lines). <b>C.</b> Performance of automated colony counting (dots) of <i>M. catarrhalis</i> CFUs on BHI plates versus the gold standard of manual counting on high performance images (X-axis). 25 plates of <i>M. catarrhalis</i> strain 25238 were used (CFU range 20–70, mean 43.9, median 42). Linear regression analysis of automated colony count versus the gold standard showed a slope of 1 (SD ±0.008; CI 0.981–1.033) for the automated colony counter. <b>D.</b> Performance of automated colony counting (dots) of <i>P. aeruginosa</i> CFUs on blood agar plates versus the gold standard of manual counting on high performance images (X-axis). 8 plates of <i>P. aeruginos</i>a clinical isolate (strain 460229) were analyzed (CFU range 1–386, mean 142.3, median 37). Linear regression analysis of automated colony count versus the gold standard showed a slope of 0.89 (SD ±0.033; CI 0.81–0.97) for the automated colony counter.</p>", "links"=>[], "tags"=>["automated"], "article_id"=>336026, "categories"=>["Information And Computing Sciences", "Chemistry", "Infectious Diseases"], "users"=>["Silvio D. Brugger", "Christian Baumberger", "Marcel Jost", "Werner Jenni", "Urs Brugger", "Kathrin Mühlemann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033695.g005", "stats"=>{"downloads"=>2, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Performance_of_the_automated_colony_counter_/336026", "title"=>"Performance of the automated colony counter.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-20 01:40:26"}

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