scholarly journals Three-dimensional imaging mass cytometry for highly multiplexed molecular and cellular mapping of tissues and the tumor microenvironment

Nature Cancer ◽  
2021 ◽  
Author(s):  
Laura Kuett ◽  
Raúl Catena ◽  
Alaz Özcan ◽  
Alex Plüss ◽  
H. R. Ali ◽  
...  
Keyword(s):  
Simultaneous Detection ◽  
Three Dimensional ◽  
3D Models ◽  
Two Dimensions ◽  
Mass Cytometry ◽  
3D Space ◽  
Tissue Organization ◽  
Holistic Understanding ◽  
Cellular Microenvironments ◽  
And Function

AbstractA holistic understanding of tissue and organ structure and function requires the detection of molecular constituents in their original three-dimensional (3D) context. Imaging mass cytometry (IMC) enables simultaneous detection of up to 40 antigens and transcripts using metal-tagged antibodies but has so far been restricted to two-dimensional imaging. Here we report the development of 3D IMC for multiplexed 3D tissue analysis at single-cell resolution and demonstrate the utility of the technology by analysis of human breast cancer samples. The resulting 3D models reveal cellular and microenvironmental heterogeneity and cell-level tissue organization not detectable in two dimensions. 3D IMC will prove powerful in the study of phenomena occurring in 3D space such as tumor cell invasion and is expected to provide invaluable insights into cellular microenvironments and tissue architecture.

scholarly journals Weighing trees with lasers: advances, challenges and opportunities

2018 ◽  
Vol 8 (2) ◽  
pp. 20170048 ◽  
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.

scholarly journals Demonstration of Three-Dimensional Indoor Visible Light Positioning with Multiple Photodiodes and Reinforcement Learning

Sensors ◽  
2020 ◽  
Vol 20 (22) ◽  
pp. 6470
Author(s):  
Zhuo Zhang ◽  
Huayang Chen ◽  
Weikang Zeng ◽  
Xinlong Cao ◽  
Xuezhi Hong ◽  
...  
Keyword(s):  
Reinforcement Learning ◽  
Visible Light ◽  
Three Dimensional ◽  
Two Dimensions ◽  
Location Based Services ◽  
Positioning Accuracy ◽  
The Third ◽  
Basic Model ◽  
3D Space ◽  
3D Positioning

To provide high-quality location-based services in the era of the Internet of Things, visible light positioning (VLP) is considered a promising technology for indoor positioning. In this paper, we study a multi-photodiodes (multi-PDs) three-dimensional (3D) indoor VLP system enhanced by reinforcement learning (RL), which can realize accurate positioning in the 3D space without any off-line training. The basic 3D positioning model is introduced, where without height information of the receiver, the initial height value is first estimated by exploring its relationship with the received signal strength (RSS), and then, the coordinates of the other two dimensions (i.e., X and Y in the horizontal plane) are calculated via trilateration based on the RSS. Two different RL processes, namely RL1 and RL2, are devised to form two methods that further improve horizontal and vertical positioning accuracy, respectively. A combination of RL1 and RL2 as the third proposed method enhances the overall 3D positioning accuracy. The positioning performance of the four presented 3D positioning methods, including the basic model without RL (i.e., Benchmark) and three RL based methods that run on top of the basic model, is evaluated experimentally. Experimental results verify that obviously higher 3D positioning accuracy is achieved by implementing any proposed RL based methods compared with the benchmark. The best performance is obtained when using the third RL based method that runs RL2 and RL1 sequentially. For the testbed that emulates a typical office environment with a height difference between the receiver and the transmitter ranging from 140 cm to 200 cm, an average 3D positioning error of 2.6 cm is reached by the best RL method, demonstrating at least 20% improvement compared to the basic model without performing RL.

scholarly journals Three Dimensional Weightbearing CT Assessment of Metatarsal Osteotomies for Hallux Valgus Correction

2020 ◽  
Vol 5 (4) ◽  
pp. 2473011420S0015
Author(s):  
Jarrett D. Cain ◽  
Jordan T. Stolle ◽  
Sorin Siegler
Keyword(s):  
Hallux Valgus ◽  
Weight Bearing ◽  
Three Dimensional ◽  
3D Models ◽  
Two Dimensions ◽  
Axial Plane ◽  
Ct Scans ◽  
First Metatarsal ◽  
3D Measurements ◽  
2D And 3D

Category: Bunion; Midfoot/Forefoot Introduction/Purpose: Hallux valgus (HV) is a tri-plane deformity of the foot corresponding to a medial deviation of the first metatarsal and a lateral deviation of the hallux. Understanding key angles between bones, as well as how these deformity changes in each plane, is critical to generating pre-operative insights into the most effective surgical correction of the deformity. While two- dimenional (2D) imaging can provide some information; utilizing three-dimensional (3D) imaging can include more precise and accurate measures of hallux valgus. The purpose of this study is to evaluate the metatarsal osteotomies for correction of hallux valgus deformity in axial, coronal and sagittal plane with 2D and 3D measurements with the hypothesis that 3D measurements will provide greater accuracy of pre and post surgical changes Methods: Ten cadaveric specimens were selected and weight-bearing CT scans were taken pre operatively with an applied an axial load of 80 pounds. Midshaft osteotomies were then performed on the cadaveric specimens followed by weight-bearing CT scans taken post-operatively.3D models of the pre-operative and post-operative specimens were created and differences in pre and post operative changes were analyzed using conventional 2D and 3D models of the first metatarsal (M1), second metatarsal (M2), fifth metatarsal (M5), and proximal phalanx of the hallux (PP1) using a paired student t-test. Quantitative examination of foot and ankle offset (FAO) alignment along with congruity of first metatarsal phalangeal and first tarsometatarsal joints Results: 3D measurements of the Inter-Metatarsal (IM) Angle, was 12.3 degrees pre-opeative and 10.4 degrees post-operative with no significant differences in all three planes while the M1M5 Angle, measured between the principle axes of the first metatarsal and fifth metatarsal was 25.3 degrees pre-operative and 22.0 degrees post-operative were statistically significant with the greatest change in the axial plane. 2D measurements of the hallux valgus angle, measured the longitudineal axes of the first metatarsal and proximal phalange of the hallux was 22.6 degrees pre opereative and 21.7 degrees post opereative with no statistical difference while the metatarsal parabola, measured in two dimensions projected onto the axial plane was 157.1 degrees before and 141.5 degrees after surgery was statistical significant. Conclusion: When comparing 2D and 3D pre and post surgical hallux valgus values, the only significant differences were identified in the absolute M1M5 values in the axial plane and a significant change was also observed in the metatarsal parabola angle. While the metatarsal parabola angle are sensitive measures, these results suggest that the M1 M5 angle allows for precise, efficient measurements in axial, coronal and sagittal planes that is previously unknown through two-dimensional radiographic measurements for quantifying the effect of metatarsal osteotomies on hallux valgus

Weight-bearing CT Technology in Musculoskeletal Pathologies of the Lower Limbs: Techniques, Initial Applications, and Preliminary Combinations with Gait-Analysis Measurements at the Istituto Ortopedico Rizzoli

2019 ◽  
Vol 23 (06) ◽  
pp. 643-656 ◽  
Author(s):  
Alberto Leardini ◽  
Stefano Durante ◽  
Claudio Belvedere ◽  
Paolo Caravaggi ◽  
Claudio Carrara ◽  
...  
Keyword(s):  
Weight Bearing ◽  
Three Dimensional ◽  
3D Models ◽  
Two Dimensions ◽  
Lower Limbs ◽  
Flat Foot ◽  
Musculoskeletal Radiology ◽  
Foot Bones ◽  
Patellofemoral Alignment ◽  
3D Scans

AbstractMusculoskeletal radiology has been mostly limited by the option between imaging under load but in two dimensions (i.e., radiographs) and three-dimensional (3D) scans but in unloaded conditions (i.e., computed tomography [CT] and magnetic resonance imaging in a supine position). Cone-beam technology is now also a way to image the extremities with 3D and weight-bearing CT. This article discusses the initial experience over a few studies in progress at an orthopaedic center. The custom design of total ankle replacements, the patellofemoral alignment after medial ligament reconstruction, the overall architecture of the foot bones in the diabetic foot, and the radiographic assessment of the rearfoot after subtalar fusion for correction of severe flat foot have all taken advantage of the 3D and weight-bearing feature of relevant CT scans. To further support these novel assessments, techniques have been developed to obtain 3D models of the bones from the scans and to merge these with state-of-the-art gait analyses.

scholarly journals Three-Dimensional Analysis of the Curvature of the Femoral Canal in 426 Chinese Femurs

2015 ◽  
Vol 2015 ◽  
pp. 1-8 ◽  
Author(s):  
Xiu-Yun Su ◽  
Zhe Zhao ◽  
Jing-Xin Zhao ◽  
Li-Cheng Zhang ◽  
An-Hua Long ◽  
...  
Keyword(s):  
Sagittal Plane ◽  
Three Dimensional ◽  
3D Models ◽  
Medullary Canal ◽  
Femoral Length ◽  
3D Space ◽  
Positive Correlations ◽  
And Gender ◽  
Banking Angle ◽  
Anatomical Parameters

Purpose. The human femur has long been considered to have an anatomical anterior curvature in the sagittal plane. We established a new method to evaluate the femoral curvature in three-dimensional (3D) space and reveal its influencing factors in Chinese population. Methods. 3D models of 426 femurs and the medullary canal were constructed using Mimics software. We standardized the positions of all femurs using 3ds Max software. After measuring the anatomical parameters, including the radius of femoral curvature (RFC) and banking angle, of the femurs using the established femur-specific coordinate system, we analyzed and determined the relationships between the anatomical parameters of the femur and the general characteristics of the population. Results. Pearson’s correlation analyses showed that there were positive correlations between the RFC and height (r=0.339, p<0.001) and the femoral length and RFC (r=0.369, p<0.001) and a negative correlation between the femoral length and banking angle (r=-0.223, p<0.001). Stepwise linear regression analyses showed that the most relevant factors for the RFC and banking angle were the femoral length and gender, respectively. Conclusions. This study concluded that the banking angle of the femur was significantly larger in female than in male.

scholarly journals Highly multiplexed molecular and cellular mapping of breast cancer tissue in three dimensions using mass tomography

2020 ◽  
Author(s):  
Raúl Catena ◽  
Alaz Özcan ◽  
Laura Kütt ◽  
Alex Plüss ◽  
Peter Schraml ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Cellular Heterogeneity ◽  
Cancer Tissue ◽  
Tissue Architecture ◽  
Tissue Microenvironment ◽  
Tissue Organization ◽  
Holistic Understanding ◽  
Cancer Sample

ABSTRACTA holistic understanding of tissue and organ structures and their functions requires the detection of molecular constituents in their original three-dimensional (3D) context. Imaging mass cytometry (IMC) makes possible the detection of up to 40 antigens and specific nucleic acids simultaneously using metal-tagged antibodies or nucleic acid probes, respectively, but has so far been restricted to two-dimensional imaging. To enable use of IMC for 3D tissue analyses, we developed mass tomography, which combines quasi deformation-free serial sectioning with novel computational methods. We utilized mass tomography to analyze a breast cancer sample. The resulting 3D representation reveals spatial and cellular heterogeneity, preferential cell-to-cell interactions, detailed tissue-architecture motifs, and the unique microenvironment of a micro-invasion, where micro-metastases clonality is examined, showing that cells arising from the same invasive area, displaying very distinct phenotypes, are all able to produce initial invasive lesions. Mass tomography will provide invaluable insights into the tissue microenvironment, cellular neighborhoods, and tissue organization.

scholarly journals Understanding and Creating 3D Forms Using Familiar Objects

2016 ◽  
Vol 4 (1) ◽  
pp. 1-8
Author(s):  
Mithra Zahedi
Keyword(s):  
Design Process ◽  
Three Dimensional ◽  
3D Models ◽  
Learning By Doing ◽  
Two Dimensions ◽  
Project Based Learning ◽  
Basic Knowledge ◽  
First Semester ◽  
Spatial Geometry ◽  
High Level

A fundamental for first-year design students is to express ideas by drawing and creating volumetric models. Traditionally, this education includes spatial geometry and generation of forms whereby students learn to appreciate intersections of volumes and projections to describe three-dimensional (3D) forms in two dimensions. However, given the aptitude of today’s students to operate 3D-modelling software and the general accessibility of current technology, spatial geometry as a core subject may seem less relevant. Our goal is to re-engage students in learning required basic knowledge and skills through a complex multifaceted design process. We have designed a first-semester course of four project-based learning activities that apply learning-by-doing methodology. For each of the past three years, 65 to 75 students have participated in our 3D Expression studio course, in which they develop understanding of design process, vocabulary, and skills to create 3D models with precision, refinements, and high-level visual impact. This paper reports on the successful results of activities conducted during the 14 full days of this studio course.

Conformation of Ribosomes from Escherichia Coli

1974 ◽  
Vol 32 ◽  
pp. 210-211
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Binding Sites ◽  
Ribosomal Proteins ◽  
Fluorescent Dyes ◽  
Protein Biosynthesis ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Dimensional Structure ◽  
Complete Understanding ◽  
And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

Structure and function of neural networks in the retina

1988 ◽  
Vol 46 ◽  
pp. 26-27
Author(s):  
Peter Sterling
Keyword(s):  
Ganglion Cells ◽  
Three Dimensional ◽  
Structure And Function ◽  
Synaptic Connections ◽  
Visual Axis ◽  
One Dimensional ◽  
Cat Retina ◽  
Ultrathin Sections ◽  
And Function ◽  
Insight Into

The synaptic connections in cat retina that link photoreceptors to ganglion cells have been analyzed quantitatively. Our approach has been to prepare serial, ultrathin sections and photograph en montage at low magnification (˜2000X) in the electron microscope. Six series, 100-300 sections long, have been prepared over the last decade. They derive from different cats but always from the same region of retina, about one degree from the center of the visual axis. The material has been analyzed by reconstructing adjacent neurons in each array and then identifying systematically the synaptic connections between arrays. Most reconstructions were done manually by tracing the outlines of processes in successive sections onto acetate sheets aligned on a cartoonist's jig. The tracings were then digitized, stacked by computer, and printed with the hidden lines removed. The results have provided rather than the usual one-dimensional account of pathways, a three-dimensional account of circuits. From this has emerged insight into the functional architecture.

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