3D reconstruction of histological sections: Application to mammary gland tissue

Arganda‐Carreras, Ignacio; Fernández-González, Rodrigo; Muñoz-Barrutia, Arrate; Ortiz‐de‐Solórzano, Carlos

doi:10.1002/jemt.20829

Cited by 583 publications

(459 citation statements)

References 33 publications

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“…Once executed, the plugin produces a data table with the following skeleton parameters: #branches, #junctions, #end-point voxels, average branch length, #triple points, #quadruple points, and maximum branch length. For a detailed description of all possible output parameters please refer tohttp://fiji.sc/wiki/index.php/ AnalyzeSkeleton and related articles [29][30][31] . A typical data table output is shown in Figure 7A.…”

Section: Representative Resultsmentioning

confidence: 99%

Analysis of Tubular Membrane Networks in Cardiac Myocytes from Atria and Ventricles

Wagner

Brandenburg

Kohl

et al. 2014

JoVE

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In cardiac myocytes a complex network of membrane tubules -the transverse-axial tubule system (TATS) -controls deep intracellular signaling functions. While the outer surface membrane and associated TATS membrane components appear to be continuous, there are substantial differences in lipid and protein content. In ventricular myocytes (VMs), certain TATS components are highly abundant contributing to rectilinear tubule networks and regular branching 3D architectures. It is thought that peripheral TATS components propagate action potentials from the cell surface to thousands of remote intracellular sarcoendoplasmic reticulum (SER) membrane contact domains, thereby activating intracellular Ca 2+ release units (CRUs). In contrast to VMs, the organization and functional role of TATS membranes in atrial myocytes (AMs) is significantly different and much less understood. Taken together, quantitative structural characterization of TATS membrane networks in healthy and diseased myocytes is an essential prerequisite towards better understanding of functional plasticity and pathophysiological reorganization.Here, we present a strategic combination of protocols for direct quantitative analysis of TATS membrane networks in living VMs and AMs. For this, we accompany primary cell isolations of mouse VMs and/or AMs with critical quality control steps and direct membrane staining protocols for fluorescence imaging of TATS membranes. Using an optimized workflow for confocal or superresolution TATS image processing, binarized and skeletonized data are generated for quantitative analysis of the TATS network and its components. Unlike previously published indirect regional aggregate image analysis strategies, our protocols enable direct characterization of specific components and derive complex physiological properties of TATS membrane networks in living myocytes with high throughput and open access software tools. In summary, the combined protocol strategy can be readily applied for quantitative TATS network studies during physiological myocyte adaptation or disease changes, comparison of different cardiac or skeletal muscle cell types, phenotyping of transgenic models, and pharmacological or therapeutic interventions.

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Section: Representative Resultsmentioning

confidence: 99%

Analysis of Tubular Membrane Networks in Cardiac Myocytes from Atria and Ventricles

Wagner

Brandenburg

Kohl

et al. 2014

JoVE

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“…Analyse Skeleton Calculates branch length and counts junctions [22] Anisotropy Estimates degree of anisotropy (DA) using the mean intercept length [13] Connectivity Uses the Euler characteristic to calculate connectivity density (Conn.D) [23,24] Fractal Dimension Estimates the fractal dimension (FD) with the box counting method [25] Isosurface Measures bone surface area (BS) and displays the surface in 3D…”

Section: Command Summarymentioning

confidence: 99%

BoneJ: Free and extensible bone image analysis in ImageJ

Doube

Kłosowski

Arganda‐Carreras

et al. 2010

Bone

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Bone geometry is commonly measured on computed tomographic (CT) and X-ray microtomographic (μCT) images. We obtained hundreds of CT, μCT and synchrotron μCT images of bones from diverse species that needed to be analysed remote from scanning hardware, but found that available software solutions were expensive, inflexible or methodologically opaque. We implemented standard bone measurements in a novel ImageJ plugin, BoneJ, with which we analysed trabecular bone, whole bones and osteocyte lacunae. BoneJ is open source and free for anyone to download, use, modify and distribute.

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“…To map how individual cells grew, cell outlines were analyzed using the AnalyzeSkeleton plug-in in Fiji (Arganda-Carreras et al, 2010). The positions of wall junctions between neighboring cells, length of the anticlinal wall segments between two wall junctions, and the Euclidean distance between wall junctions were identified.…”

Section: Cell Shape Metricsmentioning

confidence: 99%