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

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.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-251) contains supplementary material, which is available to authorized users.     

Habitability of Enceladus: Planetary Conditions for Life

The prolific activity and presence of a plume on Saturn's tiny moon Enceladus offers us a unique opportunity to sample the interior composition of an icy satellite, and to look for interesting chemistry and possible signs of life. Based on studies of the potential habitability of Jupiter's moon Europa, icy satellite oceans can be habitable if they are chemically mixed with the overlying ice shell on Myr time scales. We hypothesize that Enceladus' plume, tectonic processes, and possible liquid water ocean may create a complete and sustainable geochemical cycle that may allow it to support life. We discuss evidence for surface/ocean material exchange on Enceladus based on the amounts of silicate dust material present in the Enceladus' plume particles. Microphysical cloud modeling of Enceladus' plume shows that the particles originate from a region of Enceladus' near surface where the temperature exceeds 190 K. This could be consistent with a shear-heating origin of Enceladus' tiger stripes, which would indicate extremely high temperatures ( approximately 250-273 K) in the subsurface shear fault zone, leading to the generation of subsurface liquid water, chemical equilibration between surface and subsurface ices, and crustal recycling on a time scale of 1 to 5 Myr. Alternatively, if the tiger stripes form in a mid-ocean-ridge-type mechanism, a half-spreading rate of 1 m/year is consistent with the observed regional heat flux of 250 mW m(-2) and recycling of south polar terrain crust on a 1 to 5 Myr time scale as well.