Modeling, validation and verification of three-dimensional cell-scaffold contacts from terabyte-sized images.
Modeling, validation and verification of three-dimensional cell-scaffold contacts from terabyte-sized images.
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DOI：
10.1186/s12859-017-1928-x
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发表时间：
2017-11-28
影响因子：
3
通讯作者：
Sriram RD
中科院分区：
文献类型：
--
作者：
Bajcsy P;Yoon S;Florczyk SJ;Hotaling NA;Simon M;Szczypinski PM;Schaub NJ;Simon CG Jr;Brady M;Sriram RD
Cell-scaffold contact measurements are derived from pairs of co-registered volumetric fluorescent confocal laser scanning microscopy (CLSM) images (z-stacks) of stained cells and three types of scaffolds (i.e., spun coat, large microfiber, and medium microfiber). Our analysis of the acquired terabyte-sized collection is motivated by the need to understand the nature of the shape dimensionality (1D vs 2D vs 3D) of cell-scaffold interactions relevant to tissue engineers that grow cells on biomaterial scaffolds. We designed five statistical and three geometrical contact models, and then down-selected them to one from each category using a validation approach based on physically orthogonal measurements to CLSM. The two selected models were applied to 414 z-stacks with three scaffold types and all contact results were visually verified. A planar geometrical model for the spun coat scaffold type was validated from atomic force microscopy images by computing surface roughness of 52.35 nm ±31.76 nm which was 2 to 8 times smaller than the CLSM resolution. A cylindrical model for fiber scaffolds was validated from multi-view 2D scanning electron microscopy (SEM) images. The fiber scaffold segmentation error was assessed by comparing fiber diameters from SEM and CLSM to be between 0.46% to 3.8% of the SEM reference values. For contact verification, we constructed a web-based visual verification system with 414 pairs of images with cells and their segmentation results, and with 4968 movies with animated cell, scaffold, and contact overlays. Based on visual verification by three experts, we report the accuracy of cell segmentation to be 96.4% with 94.3% precision, and the accuracy of cell-scaffold contact for a statistical model to be 62.6% with 76.7% precision and for a geometrical model to be 93.5% with 87.6% precision. The novelty of our approach lies in (1) representing cell-scaffold contact sites with statistical intensity and geometrical shape models, (2) designing a methodology for validating 3D geometrical contact models and (3) devising a mechanism for visual verification of hundreds of 3D measurements. The raw and processed data are publicly available from https://isg.nist.gov/deepzoomweb/data/ together with the web -based verification system. The online version of this article (doi:10.1186/s12859-017-1928-x) contains supplementary material, which is available to authorized users.
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影响因子：
3
作者：
Bajcsy P;Cardone A;Chalfoun J;Halter M;Juba D;Kociolek M;Majurski M;Peskin A;Simon C;Simon M;Vandecreme A;Brady M
通讯作者：
Brady M
影响因子：
3.7
作者：
Lin, G;Adiga, U;Roysam, B
通讯作者：
Roysam, B
影响因子：
2.7
作者：
Crowley, MR;Head, KL;Asch, BB
通讯作者：
Asch, BB
影响因子：
3.4
作者：
Comeau, Jonathan W. D.;Costantino, Santiago;Wiseman, Paul W.
通讯作者：
Wiseman, Paul W.
影响因子：
41.2
作者：
Khetan S;Guvendiren M;Legant WR;Cohen DM;Chen CS;Burdick JA
通讯作者：
Burdick JA