Deconvolving Active Contours for Fluorescence Microscopy Images

Helmuth, Jo A.; Sbalzarini, Ivo F.

doi:10.1007/978-3-642-10331-5_51

Cited by 16 publications

(22 citation statements)

References 14 publications

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“…The fitting algorithm used an active contour (42), in which the surface is modeled as an elastic sheet interacting with an external energy potential that depends on the image. To account for blurring due to imaging, we created a likelihood model to serve as the potential (43). The contour was iteratively convolved with the 3D point spread function and then moved to decrease the squared difference between the original image and the convolution result.…”

Section: Methodssupporting

confidence: 40%

Rod-like bacterial shape is maintained by feedback between cell curvature and cytoskeletal localization

Ursell

Nguyen

Monds

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

228

316

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Cells typically maintain characteristic shapes, but the mechanisms of self-organization for robust morphological maintenance remain unclear in most systems. Precise regulation of rod-like shape in Escherichia coli cells requires the MreB actin-like cytoskeleton, but the mechanism by which MreB maintains rod-like shape is unknown. Here, we use time-lapse and 3D imaging coupled with computational analysis to map the growth, geometry, and cytoskeletal organization of single bacterial cells at subcellular resolution. Our results demonstrate that feedback between cell geometry and MreB localization maintains rod-like cell shape by targeting cell wall growth to regions of negative cell wall curvature. Pulsechase labeling indicates that growth is heterogeneous and correlates spatially and temporally with MreB localization, whereas MreB inhibition results in more homogeneous growth, including growth in polar regions previously thought to be inert. Biophysical simulations establish that curvature feedback on the localization of cell wall growth is an effective mechanism for cell straightening and suggest that surface deformations caused by cell wall insertion could direct circumferential motion of MreB. Our work shows that MreB orchestrates persistent, heterogeneous growth at the subcellular scale, enabling robust, uniform growth at the cellular scale without requiring global organization.bacterial cytoskeleton | biophysical modeling | morphogenesis H ow cells maintain stable and defined morphologies is a fundamental question in all branches of life. Building cellularscale structures with the correct spatial architecture and mechanical properties requires that nanometer-scale proteins have the ability to detect and alter cell shape across multiple length scales. In walled organisms such as plants (1-5), fungi (6), and bacteria (7-10), morphogenesis is often achieved through an interplay between the cytoskeleton and cell wall synthesis. A central challenge in bacterial physiology is to understand the feedback between cell shape and the coordination of wall growth by the cytoskeleton.The cell wall plays a critical mechanical role in balancing turgor stress in virtually all bacteria and is both necessary and sufficient to define cell shape (11). The bacterial cell wall is a mesh-like network of sugar strands cross-linked by peptides (11,12). In rod-shaped Escherichia coli cells, cell wall growth occurs along the cylindrical body. Biophysical modeling has suggested that a random pattern of insertion cannot preserve cell shape (13), indicating that spatial coordination of the growth machinery is necessary for cell shape maintenance. Several lines of evidence demonstrate that the actin homolog MreB (14, 15) plays a major role in this coordination in most rod-shaped bacteria. The small molecule A22 depolymerizes MreB and causes a gradual transition from a rod-like to a spherical shape (15)(16)(17). This observation suggests that the disruption of MreB changes the patterning of new material insertion, although the nature of this...

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Section: Methodssupporting

confidence: 40%

Rod-like bacterial shape is maintained by feedback between cell curvature and cytoskeletal localization

Ursell

Nguyen

Monds

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

228

316

View full text Add to dashboard Cite

show abstract

“…The corresponding energy functionals are often non-convex, as for example the piecewise smooth MS energy [2], [8] or a deconvolving energy [9]. Segmentations are found as regularized local minimizers, formalized in the framework of deformable models.…”

supporting

confidence: 42%

“…The former allows including prior knowledge about the image-formation process (e.g., the point-spread function of a microscope in deconvolving active contours [9]) and the morphology of the imaged objects. The latter allows including prior knowledge about whether FG regions are allowed to fuse or split (or both or none) during the energy minimization process [1], [27], [28].…”

Section: B Algorithmmentioning

confidence: 49%

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Discrete Region Competition for Unknown Numbers of Connected Regions

Cardinale

Paul

Sbalzarini

2012

IEEE Trans. on Image Process.

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We present a discrete, unsupervised multi-regioncompetition algorithm for image segmentation over different energy functionals. The number of regions present in an image does not need to be known a priori, nor their photometric properties. The algorithm jointly estimates the number of regions, their photometries, and their contours. The required regularization is provided by defining a region as a connected set of pixels. The evolving contours in the image are represented by computational particles that move as driven by an energy-minimization algorithm. We present an efficient discrete algorithm that allows minimizing a range of well-known energy functionals under the topological constraint of regions being connected components.

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“…Convolving the surface with the 3D point-spread function (PSF) of our microscope creates a test image that can be compared directly with the image stack from the microscope. The surface was then iteratively deformed to minimize the square difference between the simulated image and the real image (22). The PSF was measured by averaging image stacks of multiple individual 0.1 mm TetraSpeck microspheres (1000-4000) imaged at 100 nm steps in the axial direction.…”

Section: D Cell Shape Reconstructionmentioning

confidence: 99%

MreB Orientation Correlates with Cell Diameter in Escherichia coli

Ouzounov

Nguyen

Bratton

et al. 2016

Biophysical Journal

117

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Bacteria have remarkably robust cell shape control mechanisms. For example, cell diameter only varies by a few percent across a given population. The bacterial actin homolog, MreB, is necessary for establishment and maintenance of rod shape although the detailed properties of MreB that are important for shape control remained unknown. In this study, we perturb MreB in two ways: by treating cells with the polymerization-inhibiting drug A22 and by creating point mutants in mreB. These perturbations modify the steady-state diameter of cells over a wide range, from 790 5 30 nm to 1700 5 20 nm. To determine which properties of MreB are important for diameter control, we correlated structural characteristics of fluorescently tagged MreB polymers with cell diameter by simultaneously analyzing three-dimensional images of MreB and cell shape. Our results indicate that the helical pitch angle of MreB inversely correlates with the cell diameter of Escherichia coli. Other correlations between MreB and cell diameter are not found to be significant. These results demonstrate that the physical properties of MreB filaments are important for shape control and support a model in which MreB organizes the cell wall growth machinery to produce a chiral cell wall structure and dictate cell diameter.

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Deconvolving Active Contours for Fluorescence Microscopy Images

Cited by 16 publications

References 14 publications

Rod-like bacterial shape is maintained by feedback between cell curvature and cytoskeletal localization

Rod-like bacterial shape is maintained by feedback between cell curvature and cytoskeletal localization

Discrete Region Competition for Unknown Numbers of Connected Regions

MreB Orientation Correlates with Cell Diameter in Escherichia coli

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