CellGeo: A computational platform for the analysis of shape changes in cells with complex geometries

Tsygankov, Denis; Bilancia, Colleen G.; Vitriol, Eric A.; Hahn, Klaus M.; Peifer, Mark; Elston, Timothy C.

doi:10.1083/jcb.201306067

Cited by 97 publications

(104 citation statements)

References 46 publications

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“…, 2011; Nilufar et al , 2013; Hendricusdottir and Bergmann, 2014; Tsygankov et al , 2014; Tarnok et al , 2015). Similarly, image analysis tools are available to measure spatiotemporal protein concentration in cellular structures such as the leading edge (Machacek et al , 2009; Barry et al , 2015).…”

Section: Introductionmentioning

confidence: 99%

“…Excellent software solutions have been published to determine cell shape (Blum, 1967; Styner et al , 2003; Xiong et al , 2010; Tsygankov et al , 2014) and/or analyze filopodial density, elongation speed, or form (Styner et al , 2003; Costantino et al , 2008; Fanti et al. , 2011; Nilufar et al , 2013; Hendricusdottir and Bergmann, 2014; Tsygankov et al , 2014; Tarnok et al , 2015).…”

Section: Introductionmentioning

confidence: 99%

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Automated analysis of filopodial length and spatially resolved protein concentration via adaptive shape tracking

Saha

Rathmann

Viplav

et al. 2016

MBoC

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Automated analysis of filopodial length and spatially resolved protein concentration via adaptive shape tracking

Saha

Rathmann

Viplav

et al. 2016

MBoC

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“…However, these approaches are still hard to apply to cells with highly dynamic protrusions such as filopodia. In such cases, a pre-processing step that extracts the underlying cell body might be required(Tsygankov et al, 2014). …”

Section: Automated Classification Of Cell Motion Typesmentioning

confidence: 99%

“…For the pre-processing step, segmenting cells and acquiring cell masks, any image processing software, such as ImageJ or MetaMorph, will work. However, for the sake of completeness, we included a simple segmentation module MovThresh , originally developed as a part of the CellGeo package for quantification of cellular protrusion dynamics(Tsygankov et al, 2014). Accurate delineation of the cell boundary is critical; the quality of our analysis is dependent on the quality of the original image and cell segmentation.…”

Section: Gui For Morphodynamics Classification and Ready Representatimentioning

confidence: 99%

User-friendly tools for quantifying the dynamics of cellular morphology and intracellular protein clusters

Tsygankov

Chu

Chen

et al. 2014

Methods in Cell Biology

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Understanding the heterogeneous dynamics of cellular processes requires not only tools to visualize molecular behavior, but also versatile approaches to extract and analyze the information contained in live-cell movies of many cells. Automated identification and tracking of cellular features enables thorough and consistent comparative analyses in a high-throughput manner. Here we present tools for two challenging problems in computational image analysis: 1) classification of motion for cells with complex shapes and dynamics, and 2) segmentation of clustered cells and quantification of intracellular protein distributions based on a single fluorescence channel. We describe these methods, and user-friendly software* (MATLAB applications with Graphical User Interfaces) so these tools can be readily applied without an extensive knowledge of computational techniques.

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“…Because the microscope and the staining method did not provide sufficient resolution for automatic shape detection, such as that described in Tsygankov et al (17), a manual approach was taken. The bitmap image was imported into GIMP 2.8 (GNU Image Manipulation Program, freeware; http://www.gimp.com) and the edges of 91 cells and their nuclei were manually traced to generate a binary mask (Fig.…”

Section: Image Processing and Mesh Generationmentioning

confidence: 99%

Modeling of Transmembrane Potential in Realistic Multicellular Structures before Electroporation

Murovec

Sweeney

Latouche

et al. 2016

Biophysical Journal

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Many approaches for studying the transmembrane potential (TMP) induced during the treatment of biological cells with pulsed electric fields have been reported. From the simple analytical models to more complex numerical models requiring significant computational resources, a gamut of methods have been used to recapitulate multicellular environments in silico. Cells have been modeled as simple shapes in two dimensions as well as more complex geometries attempting to replicate realistic cell shapes. In this study, we describe a method for extracting realistic cell morphologies from fluorescence microscopy images to generate the piecewise continuous mesh used to develop a finite element model in two dimensions. The preelectroporation TMP induced in tightly packed cells is analyzed for two sets of pulse parameters inspired by clinical irreversible electroporation treatments. We show that high-frequency bipolar pulse trains are better, and more homogeneously raise the TMP of tightly packed cells to a simulated electroporation threshold than conventional irreversible electroporation pulse trains, at the expense of larger applied potentials. Our results demonstrate the viability of our method and emphasize the importance of considering multicellular effects in the numerical models used for studying the response of biological tissues exposed to electric fields.

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CellGeo: A computational platform for the analysis of shape changes in cells with complex geometries

Abstract: The open source MATLAB application CellGeo is a user-friendly computational platform that allows simultaneous, automated tracking and analysis of dynamic changes in cell shape, including protrusions ranging from filopodia to lamellipodia to growth cones.

Cited by 97 publications

References 46 publications

Automated analysis of filopodial length and spatially resolved protein concentration via adaptive shape tracking

Automated analysis of filopodial length and spatially resolved protein concentration via adaptive shape tracking

User-friendly tools for quantifying the dynamics of cellular morphology and intracellular protein clusters

Modeling of Transmembrane Potential in Realistic Multicellular Structures before Electroporation

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