Coupled edge profile active contours for red blood cell flow analysis

Ersoy, Ilker; Bunyak, Filiz; Higgins, John M.; Palaniappan, Kannappan

doi:10.1109/isbi.2012.6235656

Cited by 28 publications

(26 citation statements)

References 15 publications

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“…The long tracks obtained from BCTracker enable characterization of reversal frequencies of cells that would not be possible with short tracklets. BCTracker expands upon our previous work in image-based cell motility analysis [37,45,46]. The key features of BCTracker that can address deformable motion and gliding behaviour across multiple scales ranging from individual bacteria, clusters, and populations are: (i) the use of a of Kalman filter to model bending shape; (ii) use of spatial context through steric relationships between cells to handle high densities and (iii) combined use of active contours with explicit correspondence analysis to support accurate segmentation and tracking of deformable rod-like shapes.…”

Section: Experiments and Trackingmentioning

confidence: 89%

Directional reversals enableMyxococcus xanthuscells to produce collective one-dimensional streams during fruiting-body formation

Thutupalli

Sun

Bunyak

et al. 2015

J. R. Soc. Interface.

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The formation of a collectively moving group benefits individuals within a population in a variety of ways. The surface-dwelling bacterium Myxococcus xanthus forms dynamic collective groups both to feed on prey and to aggregate during times of starvation. The latter behaviour, termed fruiting-body formation, involves a complex, coordinated series of density changes that ultimately lead to three-dimensional aggregates comprising hundreds of thousands of cells and spores. How a loose, two-dimensional sheet of motile cells produces a fixed aggregate has remained a mystery as current models of aggregation are either inconsistent with experimental data or ultimately predict unstable structures that do not remain fixed in space. Here, we use high-resolution microscopy and computer vision software to spatiotemporally track the motion of thousands of individuals during the initial stages of fruiting-body formation. We find that cells undergo a phase transition from exploratory flocking, in which unstable cell groups move rapidly and coherently over long distances, to a reversal-mediated localization into onedimensional growing streams that are inherently stable in space. These observations identify a new phase of active collective behaviour and answer a long-standing open question in Myxococcus development by describing how motile cell groups can remain statistically fixed in a spatial location.

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Section: Experiments and Trackingmentioning

confidence: 89%

Directional reversals enableMyxococcus xanthuscells to produce collective one-dimensional streams during fruiting-body formation

Thutupalli

Sun

Bunyak

et al. 2015

J. R. Soc. Interface.

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“…To identify individual fibrils a shape analysis and cluster decomposition module is developed as based on previously reported modules. (Ersoy, Bunyak et al 2012, Sun, Huang et al 2014) Specifically, first connected component labeling was applied to the detection mask and disconnected blobs were identified. Then, to each detected blob B i , an ellipse E i was fitted.…”

Section: Methodsmentioning

confidence: 99%

Development of a novel in vivo corneal fibrosis model in the dog

Gronkiewicz

Giuliano

Kuroki

et al. 2016

Experimental Eye Research

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The aim of this study was to develop a novel in vivo corneal model of fibrosis in dogs utilizing alkali burn and determine the ability of suberanilohydroxamic acid (SAHA) to inhibit corneal fibrosis using this large animal model. To accomplish this, we used seven research Beagle dogs. An axial corneal alkali burn in dogs was created using 1 N NaOH topically. Six dogs were randomly and equally assigned into 2 groups: A) vehicle (DMSO, 2 μL/mL); B) anti-fibrotic treatment (50 μM SAHA). The degree of corneal opacity, ocular health, and anti-fibrotic effects of SAHA were determined utilizing the Fantes grading scale, modified McDonald-Shadduck (mMS) scoring system, optical coherence tomography (OCT), corneal histopathology, immunohistochemistry (IHC), and transmission electron microscopy (TEM). The used alkali burn dose to produce corneal fibrosis was well tolerated as no significant difference in mMS scores between control and treatment groups (p=0.89) were detected. The corneas of alkali burned dogs showed significantly greater levels of α-smooth muscle actin, the fibrotic marker, than the controls (p=0.018). Total corneal thickness of all dogs post-burn was significantly greater than baseline OCT images irrespective of treatment (p=0.004); TEM showed that alkali burned corneas had significantly greater minimum and maximum interfibrillar distances than the controls (p=0.026, p=0.018). The tested topical corneal alkali burn dose generated significant opacity and fibrosis in dog corneas without damaging the limbus as evidenced by histopathology, IHC, TEM, and OCT findings, and represents a viable large animal corneal fibrosis in vivo model. Additional in vivo SAHA dosing studies with larger sample size are warranted.

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“…Several methods based on morphological filters and watershed algorithm were proposed to detect cells or cell nuclei in fluorescence images [28][29][30][31][32]. The active contour models [33][34][35][36][37][38][39][40][41][42][43] became popular for automatic cell/nuclei segmentation at the beginning of this century when the classical CV model [33] was proposed. THG images, with Raman and other nonlinear microscopy images, differ from labeled-fluorescence images in their complexity, inherent to their high information density [5,6,20,21,24,25,[44][45][46][47]62].…”

Section: Introductionmentioning

confidence: 99%

Quantitative comparison of 3D third harmonic generation and fluorescence microscopy images

Zhang

Kuzmin

Groot

et al. 2017

Journal of Biophotonics

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Third harmonic generation (THG) microscopy is a label-free imaging technique that shows great potential for rapid pathology of brain tissue during brain tumor surgery. However, the interpretation of THG brain images should be quantitatively linked to images of more standard imaging techniques, which so far has been done qualitatively only. We establish here such a quantitative link between THG images of mouse brain tissue and all-nuclei-highlighted fluorescence images, acquired simultaneously from the same tissue area. For quantitative comparison of a substantial pair of images, we present here a segmentation workflow that is applicable for both THG and fluorescence images, with a precision of 91.3 % and 95.8 % achieved respectively. We find that the correspondence between the main features of the two imaging modalities amounts to 88.9 %, providing quantitative evidence of the interpretation of dark holes as brain cells. Moreover, 80 % bright objects in THG images overlap with nuclei highlighted in the fluorescence images, and they are 2 times smaller than the dark holes, showing that cells of different morphologies can be recognized in THG images. We expect that the described quantitative comparison is applicable to other types of brain tissue and with more specific staining experiments for cell type identification.

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Coupled edge profile active contours for red blood cell flow analysis

Cited by 28 publications

References 15 publications

Directional reversals enableMyxococcus xanthuscells to produce collective one-dimensional streams during fruiting-body formation

Directional reversals enableMyxococcus xanthuscells to produce collective one-dimensional streams during fruiting-body formation

Development of a novel in vivo corneal fibrosis model in the dog

Quantitative comparison of 3D third harmonic generation and fluorescence microscopy images

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