Quantifying Vascular Density in Tissue Engineered Constructs Using Machine Learning

Given the considerable research efforts in understanding and manipulating the vasculature in tissue health and function, making effective measurements of vascular density is critical for a variety of biomedical applications. However, because the vasculature is a heterogeneous collection of vessel segments, arranged in a complex three-dimensional architecture, which is dynamic in form and function, it is difficult to effectively measure. Here, we developed a semi-automated method that leverages machine learning to identify and quantify vascular metrics in an angiogenesis model imaged with different modalities. This software, BioSegment, is designed to make high throughput vascular density measurements of fluorescent or phase contrast images. Furthermore, the rapidity of assessments makes it an ideal tool for incorporation in tissue manufacturing workflows, where engineered tissue constructs may require frequent monitoring, to ensure that vascular growth benchmarks are met.

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Three-Dimensional Culture of Cells and Matrix Biomolecules for Engineered Tissue Development and Biokinetics Model Validation

Journal of Nanotechnology in Engineering and Medicine ◽

10.1115/1.4003878 ◽

2011 ◽

Vol 2 (2) ◽

Cited By ~ 2

Author(s):

Shelley S. Mason ◽

Sean S. Kohles ◽

Randy D. Zelick ◽

Shelley R. Winn ◽

Asit K. Saha

Keyword(s):

Three Dimensional ◽

Molecular Engineering ◽

Cartilage Tissue ◽

Tissue Development ◽

Form And Function ◽

Preliminary Validation ◽

Engineered Tissue ◽

Three Dimensional Culture ◽

Mathematical Analyses ◽

And Function

There has been considerable progress in cellular and molecular engineering due to recent advances in multiscale technology. Such technologies allow controlled manipulation of physiochemical interactions among cells in tissue culture. In particular, a novel chemomechanical bioreactor has recently been designed for the study of bone and cartilage tissue development, with particular focus on extracellular matrix formation. The bioreactor is equally significant as a tool for validation of mathematical models that explore biokinetic regulatory thresholds (Saha, A. K., and Kohles, S. S., 2010, “A Distinct Catabolic to Anabolic Threshold Due to Single-Cell Nanomechanical Stimulation in a Cartilage Biokinetics Model,” J. Nanotechnol. Eng. Med., 1(3), p. 031005; 2010, “Periodic Nanomechanical Stimulation in a Biokinetics Model Identifying Anabolic and Catabolic Pathways Associated With Cartilage Matrix Homeostasis,” J. Nanotechnol. Eng. Med., 1(4), p. 041001). In the current study, three-dimensional culture protocols are described for maintaining the cellular and biomolecular constituents within defined parameters. Preliminary validation of the bioreactor’s form and function, expected bioassays of the resulting matrix components, and application to biokinetic models are described. This approach provides a framework for future detailed explorations combining multiscale experimental and mathematical analyses, at nanoscale sensitivity, to describe cell and biomolecule dynamics in different environmental regimes.

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Probing Cytoskeletal Mechanics Using Biochemical Inhibitors

ASME 2010 Summer Bioengineering Conference, Parts A and B ◽

10.1115/sbc2010-19451 ◽

2010 ◽

Author(s):

Kenneth M. Pryse ◽

Teresa M. Abney ◽

Guy M. Genin ◽

Elliot L. Elson

Keyword(s):

Extracellular Matrix ◽

Mechanical Testing ◽

Three Dimensional ◽

Cellular Level ◽

Cellular Migration ◽

Cellular Functions ◽

Form And Function ◽

Tissue Constructs ◽

Imaging Results ◽

And Function

Quantifying the mechanics of the cytoskeletons of living cells is important for understanding several physiologic and pathologic cellular functions, such as wound healing and cellular migration in cancer. Our laboratory develops three-dimensional tissue constructs for assaying cytoskeletal mechanics in controlled conditions. These tissue constructs consist of defined components such as chick embryo fibroblasts and reconstituted rat tail collagen; fibroblasts remodel the collagen extracellular matrix (ECM) and develop a structural environment representative of that which would exist in a natural tissue. Our protocol for quantifying the microscale mechanics of the proteins that comprise the cytoskeleton involves mechanical testing of a tissue construct first in a bath that contains nutrition medium to support the active physiologic functioning of the cells, and next in the presence of inhibitors that selectively eliminate specific cytoskeletal structures. By solving an inverse homogenization problem, the mechanical functioning of these proteins at the cellular level can be estimated. Here, we present a combination of mechanical testing and imaging results to quantify the effects of specific inhibitors on cytoskeletal and extracellular matrix form and function.

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Microvascular Guidance: A Challenge to Support the Development of Vascularised Tissue Engineering Construct

The Scientific World JOURNAL ◽

10.1100/2012/201352 ◽

2012 ◽

Vol 2012 ◽

pp. 1-10 ◽

Cited By ~ 17

Author(s):

Irza Sukmana

Keyword(s):

Tissue Engineering ◽

Three Dimensional ◽

Artificial Organ ◽

Vascular Networks ◽

Tissue Constructs ◽

Future Challenges ◽

Engineered Tissue ◽

And Function ◽

Tissue Construct

The guidance of endothelial cell organization into a capillary network has been a long-standing challenge in tissue engineering. Some research efforts have been made to develop methods to promote capillary networks inside engineered tissue constructs. Capillary and vascular networks that would mimic blood microvessel function can be used to subsequently facilitate oxygen and nutrient transfer as well as waste removal. Vascularization of engineering tissue construct is one of the most favorable strategies to overpass nutrient and oxygen supply limitation, which is often the major hurdle in developing thick and complex tissue and artificial organ. This paper addresses recent advances and future challenges in developing three-dimensional culture systems to promote tissue construct vascularization allowing mimicking blood microvessel development and function encounteredin vivo. Bioreactors systems that have been used to create fully vascularized functional tissue constructs will also be outlined.

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Weighing trees with lasers: advances, challenges and opportunities

Interface Focus ◽

10.1098/rsfs.2017.0048 ◽

2018 ◽

Vol 8 (2) ◽

pp. 20170048 ◽

Cited By ~ 44

Author(s):

M. I. Disney ◽

M. Boni Vicari ◽

A. Burt ◽

K. Calders ◽

S. L. Lewis ◽

...

Keyword(s):

Laser Scanning ◽

Large Scale ◽

Three Dimensional ◽

Point Clouds ◽

3D Models ◽

Tree Form ◽

Form And Function ◽

Challenges And Opportunities ◽

And Function ◽

Non Destructive

Terrestrial laser scanning (TLS) is providing exciting new ways to quantify tree and forest structure, particularly above-ground biomass (AGB). We show how TLS can address some of the key uncertainties and limitations of current approaches to estimating AGB based on empirical allometric scaling equations (ASEs) that underpin all large-scale estimates of AGB. TLS provides extremely detailed non-destructive measurements of tree form independent of tree size and shape. We show examples of three-dimensional (3D) TLS measurements from various tropical and temperate forests and describe how the resulting TLS point clouds can be used to produce quantitative 3D models of branch and trunk size, shape and distribution. These models can drastically improve estimates of AGB, provide new, improved large-scale ASEs, and deliver insights into a range of fundamental tree properties related to structure. Large quantities of detailed measurements of individual 3D tree structure also have the potential to open new and exciting avenues of research in areas where difficulties of measurement have until now prevented statistical approaches to detecting and understanding underlying patterns of scaling, form and function. We discuss these opportunities and some of the challenges that remain to be overcome to enable wider adoption of TLS methods.

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A Customizable, Low-Cost Perfusion System for Sustaining Tissue Constructs

SLAS TECHNOLOGY Translating Life Sciences Innovation ◽

10.1177/2472630318775059 ◽

2018 ◽

Vol 23 (6) ◽

pp. 592-598

Author(s):

Brian J. O’Grady ◽

Jason X. Wang ◽

Shannon L. Faley ◽

Daniel A. Balikov ◽

Ethan S. Lippmann ◽

...

Keyword(s):

Tissue Engineering ◽

Cell Viability ◽

Large Scale ◽

Low Cost ◽

Three Dimensional ◽

Tissue Scaffolds ◽

Perfusion System ◽

Pump System ◽

Tissue Constructs ◽

Engineered Tissue

The fabrication of engineered vascularized tissues and organs requiring sustained, controlled perfusion has been facilitated by the development of several pump systems. Currently, researchers in the field of tissue engineering require the use of pump systems that are in general large, expensive, and generically designed. Overall, these pumps often fail to meet the unique demands of perfusing clinically useful tissue constructs. Here, we describe a pumping platform that overcomes these limitations and enables scalable perfusion of large, three-dimensional hydrogels. We demonstrate the ability to perfuse multiple separate channels inside hydrogel slabs using a preprogrammed schedule that dictates pumping speed and time. The use of this pump system to perfuse channels in large-scale engineered tissue scaffolds sustained cell viability over several weeks.

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Quantitative analysis of subcellular distributions with an open-source, object-based tool

Biology Open ◽

10.1242/bio.055228 ◽

2020 ◽

Vol 9 (10) ◽

pp. bio055228 ◽

Cited By ~ 2

Author(s):

Pearl V. Ryder ◽

Dorothy A. Lerit

Keyword(s):

Image Analysis ◽

Open Source ◽

Three Dimensional ◽

Analysis Data ◽

Form And Function ◽

Object Based Image Analysis ◽

Object Based ◽

And Function ◽

Microscopy Images ◽

Complete Process

ABSTRACTThe subcellular localization of objects, such as organelles, proteins, or other molecules, instructs cellular form and function. Understanding the underlying spatial relationships between objects through colocalization analysis of microscopy images is a fundamental approach used to inform biological mechanisms. We generated an automated and customizable computational tool, the SubcellularDistribution pipeline, to facilitate object-based image analysis from three-dimensional (3D) fluorescence microcopy images. To test the utility of the SubcellularDistribution pipeline, we examined the subcellular distribution of mRNA relative to centrosomes within syncytial Drosophila embryos. Centrosomes are microtubule-organizing centers, and RNA enrichments at centrosomes are of emerging importance. Our open-source and freely available software detected RNA distributions comparably to commercially available image analysis software. The SubcellularDistribution pipeline is designed to guide the user through the complete process of preparing image analysis data for publication, from image segmentation and data processing to visualization.This article has an associated First Person interview with the first author of the paper.

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Virtual paleontology: computer-aided analysis of fossil form and function

Journal of Paleontology ◽

10.1666/13-001i ◽

2014 ◽

Vol 88 (4) ◽

pp. 633-635 ◽

Cited By ~ 8

Author(s):

Imran A. Rahman ◽

Selena Y. Smith

Keyword(s):

Imaging Techniques ◽

Three Dimensional ◽

Fossil Plants ◽

Element Analysis ◽

X Ray ◽

Form And Function ◽

Wide Range ◽

History Of ◽

Micro Tomography ◽

And Function

‘Virtual paleontology’ entails the use of computational methods to assist in the three-dimensional (3-D) visualization and analysis of fossils, and has emerged as a powerful approach for research on the history of life. Three-dimensional imaging techniques allow poorly understood or previously unknown anatomies of fossil plants, invertebrates, and vertebrates, as well as microfossils and trace fossils, to be described in much greater detail than formerly possible, and are applicable to a wide range of preservation types and specimen sizes (Table 1). These methods include non-destructive high-resolution scanning technologies such as conventional X-ray micro-tomography and synchrotron-based X-ray tomography. In addition, form and function can be rigorously investigated through quantitative analysis of computer models, for example finite-element analysis.

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