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

Mekterović, Igor; Mekterović, D.; Maglica, Željka

doi:10.1186/1471-2105-15-251

Cited by 15 publications

(10 citation statements)

References 30 publications

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“…Images acquired using Resolve3D softWoRx-Acquire version 4.0.0 (Applied Precision) were exported as 16-bit TIFF files and processed using ImageJ 1.46 (NIH) and BactImAS ( 44 ). Background was subtracted from each fluorescence channel by deducting the fluorescence in a cell-free area.…”

Section: Methodsmentioning

confidence: 99%

Single-Cell Tracking Reveals Antibiotic-Induced Changes in Mycobacterial Energy Metabolism

Maglica

Özdemir

McKinney

2015

mBio

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ATP is a key molecule of cell physiology, but despite its importance, there are currently no methods for monitoring single-cell ATP fluctuations in live bacteria. This is a major obstacle in studies of bacterial energy metabolism, because there is a growing awareness that bacteria respond to stressors such as antibiotics in a highly individualistic manner. Here, we present a method for long-term single-cell tracking of ATP levels in Mycobacterium smegmatis based on a combination of microfluidics, time-lapse microscopy, and Förster resonance energy transfer (FRET)-based ATP biosensors. Upon treating cells with antibiotics, we observed that individual cells undergo an abrupt and irreversible switch from high to low intracellular ATP levels. The kinetics and extent of ATP switching clearly discriminate between an inhibitor of ATP synthesis and other classes of antibiotics. Cells that resume growth after 24 h of antibiotic treatment maintain high ATP levels throughout the exposure period. In contrast, antibiotic-treated cells that switch from ATP-high to ATP-low states never resume growth after antibiotic washout. Surprisingly, only a subset of these nongrowing ATP-low cells stains with propidium iodide (PI), a widely used live/dead cell marker. These experiments also reveal a cryptic subset of cells that do not resume growth after antibiotic washout despite remaining ATP high and PI negative. We conclude that ATP tracking is a more dynamic, sensitive, reliable, and discriminating marker of cell viability than staining with PI. This method could be used in studies to evaluate antimicrobial effectiveness and mechanism of action, as well as for high-throughput screening.

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Section: Methodsmentioning

confidence: 99%

Single-Cell Tracking Reveals Antibiotic-Induced Changes in Mycobacterial Energy Metabolism

Maglica

Özdemir

McKinney

2015

mBio

Self Cite

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“…ImageJ-based 7 or Icy-based 10 solutions, such as Coli-Inspector 2 or BactImAS 4 provide an integrated and user-friendly approach to analyze spatio-temporal localization patterns and/or intensity of fluorescent protein fusions in time-lapse movies, but are specific to certain tasks and/or organisms. Coli-Inspector, for instance, is based on ObjectJ, which provides an integrated platform that dynamically links user-defined objects, such as cell axes, cell diameters, or constriction sites across images with their corresponding properties.…”

mentioning

confidence: 99%

MicrobeJ, a tool for high throughput bacterial cell detection and quantitative analysis

2016

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Single cell analysis of bacteria and subcellular protein localization dynamics has shown that bacteria have elaborate life cycles, cytoskeletal protein networks, and complex signal transduction pathways driven by localized proteins. The volume of multi-dimensional images generated in such experiments and the computation time required to detect, associate, and track cells and subcellular features pose considerable challenges, especially for high-throughput experiments. Therefore, there is a need for a versatile, computationally efficient image analysis tool capable of extracting the desired relationships from images in a meaningful and unbiased way. Here we present MicrobeJ, a plug-in for the open-source platform ImageJ. MicrobeJ provides a comprehensive framework to process images derived from a wide variety of microscopy experiments with special emphasis on large image sets. It performs the most common intensity and morphology measurements as well as customized detection of poles, septa, fluorescent foci, and organelles, determines their sub-cellular localization with sub-pixel resolution, and tracks them over time. Because a dynamic link is maintained between the images, measurements, and all data representations derived from them, the editor and suite of advanced data presentation tools facilitates the image analysis process and provides a robust way to verify the accuracy and veracity of the data.

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“…A BactImAS (Bacterial Image Analysis Software) is an open source software that can be used for cell segmentation and tracking, as well as storage, analysis, and visualization of acquired timelapse data. The detailed procedure and application of software is described by Mekterović et al, [29].…”

Section: The Decision Systemmentioning

confidence: 99%

Design of a Smart System for Rapid Bacterial Test

Patil

Levin²,

Rajkumar³

et al. 2019

Water

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In this article, we present our initial findings to support the design of an advanced field test to detect bacterial contamination in water samples. The system combines the use of image processing and neural networks to detect an early presence of bacterial activity. We present here a proof of concept with some tests results. Our initial findings are very promising and indicate detection of viable bacterial cells within a period of 2 h. To the authors' knowledge this is the first attempt to quantify viable bacterial cells in a water sample using cell splitting. We also present a detailed design of the complete system that uses the time lapse images from a microscope to complete the design of a neural network based smart system.

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

Cited by 15 publications

References 30 publications

Single-Cell Tracking Reveals Antibiotic-Induced Changes in Mycobacterial Energy Metabolism

Single-Cell Tracking Reveals Antibiotic-Induced Changes in Mycobacterial Energy Metabolism

MicrobeJ, a tool for high throughput bacterial cell detection and quantitative analysis

Design of a Smart System for Rapid Bacterial Test

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