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Pregled bibliografske jedinice broj: 711334

BactImAS: a platform for processing and analysis of bacterial time-lapse microscopy movies


Mekterović, Igor; Mekterović, Darko; Maglica, Željka
BactImAS: a platform for processing and analysis of bacterial time-lapse microscopy movies // BMC bioinformatics, 15 (2014), 251; 1-10 doi:10.1186/1471-2105-15-251 (međunarodna recenzija, članak, znanstveni)


CROSBI ID: 711334 Za ispravke kontaktirajte CROSBI podršku putem web obrasca

Naslov
BactImAS: a platform for processing and analysis of bacterial time-lapse microscopy movies

Autori
Mekterović, Igor ; Mekterović, Darko ; Maglica, Željka

Izvornik
BMC bioinformatics (1471-2105) 15 (2014), 251; 1-10

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
time-lapse microscopy; mycobacteria; image analysis; imageJ; icy; data visualization; database

Sažetak
The software available to date for analyzing image sequences from time-lapse microscopy works only for certain bacteria and under limited conditions. These programs, mostly MATLAB-based, fail for microbes with irregular shape, indistinct cell division sites, or that grow in closely packed microcolonies. Unfortunately, many organisms of interest have these characteristics, and analyzing their image sequences has been limited to time consuming manual processing. Results Here we describe BactImAS – a modular, multi- platform, open- source, Java-based software delivered both as a standalone program and as a plugin for Icy. The software is designed for extracting and visualizing quantitative data from bacterial time- lapse movies. BactImAS uses a semi- automated approach where the user defines initial cells, identifies cell division events, and, if necessary, manually corrects cell segmentation with the help of user-friendly GUI and incorporated ImageJ application. The program segments and tracks cells using a newly-developed algorithm designed for movies with difficult-to- segment cells that exhibit small frame-to-frame differences. Measurements are extracted from images in a configurable, automated fashion and an SQLite database is used to store, retrieve, and exchange all acquired data. Finally, the BactImAS can generate configurable lineage tree visualizations and export data as CSV files. We tested BactImAS on time-lapse movies of Mycobacterium smegmatis and achieved at least 10- fold reduction of processing time compared to manual analysis. We illustrate the power of the visualization tool by showing heterogeneity of both icl expression and cell growth atop of a lineage tree. Conclusions The presented software simplifies quantitative analysis of time-lapse movies overall and is currently the only available software for the analysis of mycobacteria-like cells. It will be of interest to the community of both end-users and developers of time-lapse microscopy software.

Izvorni jezik
Engleski

Znanstvena područja
Biologija, Računarstvo



POVEZANOST RADA


Projekti:
036-0361983-2012 - Semantička integracija heterogenih izvorišta podataka (Baranović, Mirta, MZOS ) ( POIROT)

Ustanove:
Fakultet elektrotehnike i računarstva, Zagreb,
Institut "Ruđer Bošković", Zagreb

Profili:

Avatar Url Igor Mekterović (autor)

Avatar Url Darko Mekterović (autor)

Avatar Url Željka Maglica (autor)

Poveznice na cjeloviti tekst rada:

doi fulir.irb.hr www.biomedcentral.com

Citiraj ovu publikaciju:

Mekterović, Igor; Mekterović, Darko; Maglica, Željka
BactImAS: a platform for processing and analysis of bacterial time-lapse microscopy movies // BMC bioinformatics, 15 (2014), 251; 1-10 doi:10.1186/1471-2105-15-251 (međunarodna recenzija, članak, znanstveni)
Mekterović, I., Mekterović, D. & Maglica, Ž. (2014) BactImAS: a platform for processing and analysis of bacterial time-lapse microscopy movies. BMC bioinformatics, 15 (251), 1-10 doi:10.1186/1471-2105-15-251.
@article{article, author = {Mekterovi\'{c}, Igor and Mekterovi\'{c}, Darko and Maglica, \v{Z}eljka}, year = {2014}, pages = {1-10}, DOI = {10.1186/1471-2105-15-251}, keywords = {time-lapse microscopy, mycobacteria, image analysis, imageJ, icy, data visualization, database}, journal = {BMC bioinformatics}, doi = {10.1186/1471-2105-15-251}, volume = {15}, number = {251}, issn = {1471-2105}, title = {BactImAS: a platform for processing and analysis of bacterial time-lapse microscopy movies}, keyword = {time-lapse microscopy, mycobacteria, image analysis, imageJ, icy, data visualization, database} }
@article{article, author = {Mekterovi\'{c}, Igor and Mekterovi\'{c}, Darko and Maglica, \v{Z}eljka}, year = {2014}, pages = {1-10}, DOI = {10.1186/1471-2105-15-251}, keywords = {time-lapse microscopy, mycobacteria, image analysis, imageJ, icy, data visualization, database}, journal = {BMC bioinformatics}, doi = {10.1186/1471-2105-15-251}, volume = {15}, number = {251}, issn = {1471-2105}, title = {BactImAS: a platform for processing and analysis of bacterial time-lapse microscopy movies}, keyword = {time-lapse microscopy, mycobacteria, image analysis, imageJ, icy, data visualization, database} }

Časopis indeksira:


  • Current Contents Connect (CCC)
  • Web of Science Core Collection (WoSCC)
    • Science Citation Index Expanded (SCI-EXP)
    • SCI-EXP, SSCI i/ili A&HCI
  • Scopus
  • MEDLINE


Uključenost u ostale bibliografske baze podataka::


  • Ecology Abstracts


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