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Hall ME, Black MS, Gold GE, Levenston ME. Validation of watershed-based segmentation of the cartilage surface from sequential CT arthrography scans. Quant Imaging Med Surg 2022; 12:1-14. [PMID: 34993056 PMCID: PMC8666781 DOI: 10.21037/qims-20-1062] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 07/12/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND This study investigated the utility of a 2-dimensional watershed algorithm for identifying the cartilage surface in computed tomography (CT) arthrograms of the knee up to 33 minutes after an intra-articular iohexol injection as boundary blurring increased. METHODS A 2D watershed algorithm was applied to CT arthrograms of 3 bovine stifle joints taken 3, 8, 18, and 33 minutes after iohexol injection and used to segment tibial cartilage. Thickness measurements were compared to a reference standard thickness measurement and the 3-minute time point scan. RESULTS 77.2% of cartilage thickness measurements were within 0.2 mm (1 voxel) of the thickness calculated in the reference scan at the 3-minute time point. 42% fewer voxels could be segmented from the 33-minute scan than the 3-minute scan due to diffusion of the contrast agent out of the joint space and into the cartilage, leading to blurring of the cartilage boundary. The traced watershed lines were closer to the location of the cartilage surface in areas where tissues were in direct contact with each other (cartilage-cartilage or cartilage-meniscus contact). CONCLUSIONS The use of watershed dam lines to guide cartilage segmentation shows promise for identifying cartilage boundaries from CT arthrograms in areas where soft tissues are in direct contact with each other.
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Affiliation(s)
- Mary E. Hall
- Department of Mechanical Engineering, Stanford University, Stanford, CA, USA
| | - Marianne S. Black
- Department of Mechanical Engineering, Stanford University, Stanford, CA, USA
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - Garry E. Gold
- Department of Radiology, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Marc E. Levenston
- Department of Mechanical Engineering, Stanford University, Stanford, CA, USA
- Department of Radiology, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
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2
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Cao L, der Meer ADV, Verbeek FJ, Passier R. Automated image analysis system for studying cardiotoxicity in human pluripotent stem cell-Derived cardiomyocytes. BMC Bioinformatics 2020; 21:187. [PMID: 32408861 PMCID: PMC7222481 DOI: 10.1186/s12859-020-3466-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 03/23/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Cardiotoxicity, characterized by severe cardiac dysfunction, is a major problem in patients treated with different classes of anticancer drugs. Development of predictable human-based models and assays for drug screening are crucial for preventing potential drug-induced adverse effects. Current animal in vivo models and cell lines are not always adequate to represent human biology. Alternatively, human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) show great potential for disease modelling and drug-induced toxicity screenings. Fully automated high-throughput screening of drug toxicity on hiPSC-CMs by fluorescence image analysis is, however, very challenging, due to clustered cell growth patterns and strong intracellular and intercellular variation in the expression of fluorescent markers. RESULTS In this paper, we report on the development of a fully automated image analysis system for quantification of cardiotoxic phenotypes from hiPSC-CMs that are treated with various concentrations of anticancer drugs doxorubicin or crizotinib. This high-throughput system relies on single-cell segmentation by nuclear signal extraction, fuzzy C-mean clustering of cardiac α-actinin signal, and finally nuclear signal propagation. When compared to manual segmentation, it generates precision and recall scores of 0.81 and 0.93, respectively. CONCLUSIONS Our results show that our fully automated image analysis system can reliably segment cardiomyocytes even with heterogeneous α-actinin signals.
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Affiliation(s)
- Lu Cao
- Imaging and Bioinformatics group, Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Niels Bohrweg 1, Leiden, 2333 CA, The Netherlands
| | - Andries D van der Meer
- Dept of Applied Stem Cell Technologies, MIRA Institute, University of Twente, Drienerlolaan 5, Enschede, 7522 NB, The Netherlands
| | - Fons J Verbeek
- Imaging and Bioinformatics group, Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Niels Bohrweg 1, Leiden, 2333 CA, The Netherlands.
| | - Robert Passier
- Dept of Applied Stem Cell Technologies, MIRA Institute, University of Twente, Drienerlolaan 5, Enschede, 7522 NB, The Netherlands. .,Dept of Anatomy and Embryology, Leiden University Medical Center, Albinusdreef 2, Leiden, 2333 ZA, The Netherlands.
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3
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Exner T, Beretta CA, Gao Q, Afting C, Romero-Brey I, Bartenschlager R, Fehring L, Poppelreuther M, Füllekrug J. Lipid droplet quantification based on iterative image processing. J Lipid Res 2019; 60:1333-1344. [PMID: 30926625 DOI: 10.1194/jlr.d092841] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/28/2019] [Indexed: 12/15/2022] Open
Abstract
Lipid droplets (LDs) are ubiquitous and highly dynamic subcellular organelles required for the storage of neutral lipids. LD number and size distribution are key parameters affected not only by nutrient supply but also by lipotoxic stress and metabolic regulation. Current methods for LD quantification lack general applicability and are either based on time consuming manual evaluation or show limitations if LDs are high in numbers or closely clustered. Here, we present an ImageJ-based approach for the detection and quantification of LDs stained by neutral lipid dyes in images acquired by conventional wide-field fluorescence microscopy. The method features an adjustable preprocessing procedure that resolves LD clusters. LD identification is based on their circular edges and central fluorescence intensity maxima. Adaptation to different cell types is mediated by a set of interactive parameters. Validation was done for three different cell lines using manual evaluation of LD numbers and volume measurement by 3D rendering of confocal datasets. In an application example, we show that overexpression of the acyl-CoA synthetase, FATP4/ACSVL5, in oleate-treated COS7 cells increased the size of LDs but not their number.
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Affiliation(s)
- Tarik Exner
- Molecular Cell Biology Laboratory Internal Medicine IV, Heidelberg University, Heidelberg, Germany
| | - Carlo A Beretta
- CellNetworks Math-Clinic Core Facility, BioQuant Heidelberg University, Heidelberg, Germany
| | - Qi Gao
- CellNetworks Math-Clinic Core Facility, BioQuant Heidelberg University, Heidelberg, Germany
| | - Cassian Afting
- Molecular Cell Biology Laboratory Internal Medicine IV, Heidelberg University, Heidelberg, Germany
| | - Inés Romero-Brey
- Department of Infectious Diseases, Molecular Virology Heidelberg University, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology Heidelberg University, Heidelberg, Germany.,Department of Virus-Associated Carcinogenesis, German Cancer Research Center, Heidelberg, Germany
| | - Leonard Fehring
- Molecular Cell Biology Laboratory Internal Medicine IV, Heidelberg University, Heidelberg, Germany
| | - Margarete Poppelreuther
- Molecular Cell Biology Laboratory Internal Medicine IV, Heidelberg University, Heidelberg, Germany
| | - Joachim Füllekrug
- Molecular Cell Biology Laboratory Internal Medicine IV, Heidelberg University, Heidelberg, Germany
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Weis S, Schröter M. Analyzing X-ray tomographies of granular packings. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2017; 88:051809. [PMID: 28571396 DOI: 10.1063/1.4983051] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Starting from three-dimensional volume data of a granular packing, as, e.g., obtained by X-ray Computed Tomography, we discuss methods to first detect the individual particles in the sample and then analyze their properties. This analysis includes the pair correlation function, the volume and shape of the Voronoi cells, and the number and type of contacts formed between individual particles. We mainly focus on packings of monodisperse spheres, but we will also comment on other monoschematic particles such as ellipsoids and tetrahedra. This paper is accompanied by a package of free software containing all programs (including source code) and an example three-dimensional dataset which allows the reader to reproduce and modify all examples given.
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Affiliation(s)
- Simon Weis
- Institut für Theoretische Physik I, Friedrich-Alexander-Universität, 91058 Erlangen, Germany
| | - Matthias Schröter
- Institute for Multiscale Simulation, Friedrich-Alexander-Universität, 91052 Erlangen, Germany
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5
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West BM, Stuckelberger M, Jeffries A, Gangam S, Lai B, Stripe B, Maser J, Rose V, Vogt S, Bertoni MI. X-ray fluorescence at nanoscale resolution for multicomponent layered structures: a solar cell case study. JOURNAL OF SYNCHROTRON RADIATION 2017; 24:288-295. [PMID: 28009569 DOI: 10.1107/s1600577516015721] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 10/06/2016] [Indexed: 06/06/2023]
Abstract
The study of a multilayered and multicomponent system by spatially resolved X-ray fluorescence microscopy poses unique challenges in achieving accurate quantification of elemental distributions. This is particularly true for the quantification of materials with high X-ray attenuation coefficients, depth-dependent composition variations and thickness variations. A widely applicable procedure for use after spectrum fitting and quantification is described. This procedure corrects the elemental distribution from the measured fluorescence signal, taking into account attenuation of the incident beam and generated fluorescence from multiple layers, and accounts for sample thickness variations. Deriving from Beer-Lambert's law, formulae are presented in a general integral form and numerically applicable framework. The procedure is applied using experimental data from a solar cell with a Cu(In,Ga)Se2 absorber layer, measured at two separate synchrotron beamlines with varied measurement geometries. This example shows the importance of these corrections in real material systems, which can change the interpretation of the measured distributions dramatically.
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Affiliation(s)
- Bradley M West
- School of Electrical, Computer, and Energy Engineering, Arizona State University, 551 E Tyler Mall, Tempe, AZ 85281, USA
| | - Michael Stuckelberger
- School of Electrical, Computer, and Energy Engineering, Arizona State University, 551 E Tyler Mall, Tempe, AZ 85281, USA
| | - April Jeffries
- School for Engineering of Matter, Transport, and Energy, Arizona State University, 551 E Tyler Mall, Tempe, AZ 85281, USA
| | - Srikanth Gangam
- School of Electrical, Computer, and Energy Engineering, Arizona State University, 551 E Tyler Mall, Tempe, AZ 85281, USA
| | - Barry Lai
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Benjamin Stripe
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Jörg Maser
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Volker Rose
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Stefan Vogt
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Mariana I Bertoni
- School of Electrical, Computer, and Energy Engineering, Arizona State University, 551 E Tyler Mall, Tempe, AZ 85281, USA
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Eghiaian F, Rigato A, Scheuring S. Structural, mechanical, and dynamical variability of the actin cortex in living cells. Biophys J 2016; 108:1330-1340. [PMID: 25809247 DOI: 10.1016/j.bpj.2015.01.016] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 12/18/2014] [Accepted: 01/07/2015] [Indexed: 12/31/2022] Open
Abstract
In eukaryotic cells, an actin-based cortex lines the inner leaflet of the plasma membrane, endowing the cells with crucial mechanical and functional properties. Unfortunately, it has not been possible to study the structural dynamics of the actin cortex at high lateral resolution in living cells. Here, we performed atomic force microscopy time-lapse imaging and mechanical mapping of actin in the cortex of living cells at high lateral and temporal resolution. Cortical actin filaments adopted discernible arrangements, ranging from large parallel bundles with low connectivity to a tight meshwork of short filaments. Mixing of these architectures resulted in attuned cortex networks with specific connectivity, mechanical responses, and marked differences in their dynamic behavior.
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Affiliation(s)
- Frédéric Eghiaian
- U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Annafrancesca Rigato
- U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Simon Scheuring
- U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy, Marseille, France.
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Fu Y, Xi Y, Cao Y, Wang Y. X-ray microtomography study of the compaction process of rods under tapping. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:051311. [PMID: 23004754 DOI: 10.1103/physreve.85.051311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Indexed: 06/01/2023]
Abstract
We present an x-ray microtomography study of the compaction process of cylindrical rods under tapping. The process is monitored by measuring the evolution of the orientational order parameter, local, and overall packing densities as a function of the tapping number for different tapping intensities. The slow relaxation dynamics of the orientational order parameter can be well fitted with a stretched-exponential law with stretching exponents ranging from 0.9 to 1.6. The corresponding relaxation time versus tapping intensity follows an Arrhenius behavior which is reminiscent of the slow dynamics in thermal glassy systems. We also investigated the boundary effect on the ordering process and found that boundary rods order faster than interior ones. In searching for the underlying mechanism of the slow dynamics, we estimated the initial random velocities of the rods under tapping and found that the ordering process is compatible with a diffusion mechanism. The average coordination number as a function of the tapping number at different tapping intensities has also been measured, which spans a range from 6 to 8.
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Affiliation(s)
- Yang Fu
- Department of Physics, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China
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Mukhopadhyay S, Peixinho J. Packings of deformable spheres. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:011302. [PMID: 21867159 DOI: 10.1103/physreve.84.011302] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Revised: 06/17/2011] [Indexed: 05/31/2023]
Abstract
We present an experimental study of disordered packings of deformable spheres. Fluorescent hydrogel spheres immersed in water together with a tomography technique enabled the imaging of the three-dimensional arrangement. The mechanical behavior of single spheres subjected to compression is first examined. Then the properties of packings of a randomized collection of deformable spheres in a box with a moving lid are tested. The transition to a state where the packing withstands finite stresses before yielding is observed. Starting from random packed states, the power law dependence of the normal force versus packing fraction or strain at different velocities is quantified. Furthermore, a compression-decompression sequence at low velocities resulted in rearrangements of the spheres. At larger packing fractions, a saturation of the mean coordination number took place, indicating the deformation and faceting of the spheres.
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