title: BactImAS: a platform for processing and analysis of bacterial time-lapse microscopy movies.
abstract: BACKGROUND
  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.
authors: Igor
authors: I
authors: Mekterović
authors: Darko
authors: D
authors: Mekterović
authors: School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), 1015 Lausanne, Switzerland. zeljka.maglica@gmail.com.
authors: Zeljka
authors: Z
authors: Maglica
mesh_terms: D000465:Algorithms; D001426:Bacterial Proteins / Q000378:metabolism; D049109:Cell Proliferation; D016208:Databases, Factual; D015964:Gene Expression Regulation, Bacterial; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D007522:Isocitrate Lyase / Q000378:metabolism; D008853:Microscopy / Q000379:methods*; D020102:Mycobacterium smegmatis / Q000166:cytology / Q000235:genetics; D012984:Software
chemical_list: D001426:Bacterial Proteins; C402427:icl protein, Mycobacterium; D007522:Isocitrate Lyase