9
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      BacStalk: A comprehensive and interactive image analysis software tool for bacterial cell biology

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Related collections

          Most cited references35

          • Record: found
          • Abstract: found
          • Article: not found

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

          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.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            High-throughput, subpixel precision analysis of bacterial morphogenesis and intracellular spatio-temporal dynamics.

            Bacteria display various shapes and rely on complex spatial organization of their intracellular components for many cellular processes. This organization changes in response to internal and external cues. Quantitative, unbiased study of these spatio-temporal dynamics requires automated image analysis of large microscopy datasets. We have therefore developed MicrobeTracker, a versatile and high-throughput image analysis program that outlines and segments cells with subpixel precision, even in crowded images and mini-colonies, enabling cell lineage tracking. MicrobeTracker comes with an integrated accessory tool, SpotFinder, which precisely tracks foci of fluorescently labelled molecules inside cells. Using MicrobeTracker, we discover that the dynamics of the extensively studied Escherichia coli Min oscillator depends on Min protein concentration, unveiling critical limitations in robustness within the oscillator. We also find that the fraction of MinD proteins oscillating increases with cell length, indicating that the oscillator has evolved to be most effective when cells attain an appropriate length. MicrobeTracker was also used to uncover novel aspects of morphogenesis and cell cycle regulation in Caulobacter crescentus. By tracking filamentous cells, we show that the chromosomal origin at the old-pole is responsible for most replication/separation events while the others remain largely silent despite contiguous cytoplasm. This surprising position-dependent silencing is regulated by division. © 2011 Blackwell Publishing Ltd.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Oufti: an integrated software package for high-accuracy, high-throughput quantitative microscopy analysis.

              With the realization that bacteria display phenotypic variability among cells and exhibit complex subcellular organization critical for cellular function and behavior, microscopy has re-emerged as a primary tool in bacterial research during the last decade. However, the bottleneck in today's single-cell studies is quantitative image analysis of cells and fluorescent signals. Here, we address current limitations through the development of Oufti, a stand-alone, open-source software package for automated measurements of microbial cells and fluorescence signals from microscopy images. Oufti provides computational solutions for tracking touching cells in confluent samples, handles various cell morphologies, offers algorithms for quantitative analysis of both diffraction and non-diffraction-limited fluorescence signals and is scalable for high-throughput analysis of massive datasets, all with subpixel precision. All functionalities are integrated in a single package. The graphical user interface, which includes interactive modules for segmentation, image analysis and post-processing analysis, makes the software broadly accessible to users irrespective of their computational skills.
                Bookmark

                Author and article information

                Contributors
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                Journal
                Molecular Microbiology
                Mol Microbiol
                Wiley
                0950-382X
                1365-2958
                July 2020
                April 14 2020
                July 2020
                : 114
                : 1
                : 140-150
                Affiliations
                [1 ]Max Planck Institute for Terrestrial Microbiology Marburg Germany
                [2 ]Department of Biology Philipps‐Universität Marburg Germany
                [3 ]LOEWE Center for Synthetic Microbiology Marburg Germany
                [4 ]Department of Physics Philipps‐Universität Marburg Germany
                Article
                10.1111/mmi.14501
                32190923
                5e0ee366-c9a3-4b9e-a2bb-0b27e0f4ce41
                © 2020

                http://creativecommons.org/licenses/by-nc/4.0/

                http://doi.wiley.com/10.1002/tdm_license_1.1

                History

                Comments

                Comment on this article