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Spatial analysis for the distribution of cells in tissue sections

Xu, Ruibin LU (2014) In Student thesis series INES NGEM01 20141
Dept of Physical Geography and Ecosystem Science
Abstract
Spatial analysis, playing an essential role in data mining, is applied in a considerable number of fields. It is because of its broad applicability that dealing with the interdisciplinary issues is becoming more prevalent. It aims at exploring the underlying patterns of the data.

In this project, we will employ the methodology that we utilize to tackle spatial problems to investigate how the cells distribute in the infected tissue sections and if there are clusters existing among the cells. The cells that are neighboring to the viruses are of interest. The data were provided by the Medetect Company in the form of 2-dimensional point data.

We firstly adopted two common spatial analysis methods, clustering methods and proximity... (More)
Spatial analysis, playing an essential role in data mining, is applied in a considerable number of fields. It is because of its broad applicability that dealing with the interdisciplinary issues is becoming more prevalent. It aims at exploring the underlying patterns of the data.

In this project, we will employ the methodology that we utilize to tackle spatial problems to investigate how the cells distribute in the infected tissue sections and if there are clusters existing among the cells. The cells that are neighboring to the viruses are of interest. The data were provided by the Medetect Company in the form of 2-dimensional point data.

We firstly adopted two common spatial analysis methods, clustering methods and proximity methods. In addition, a method for constructing a 2-dimensional hull was developed in order to delineate the compartments in tissue sections. A binomial test was conducted to evaluate the results.

It is detectable that the clusters do exist among cells. The immune cells would accumulate around the viruses. We also found different patterns near and far away from viruses. This study implicates that the cells are interactive with each other and thus present the spatial patterns. However, our analyses are restricted in a planar circumstance instead of treating them in 3-dimensional space. For the further study, the spatial analysis could be carried out in three dimensions. (Less)
Popular Abstract
It has been popular to utilize the heuristic methods or the existing methods to discover new findings and explain the mysterious phenomena in other subjects. And it is known that everything in nature relates to each other. In this sense, we could assume that the entire distribution of objects is relative to the locations of individuals. The idea of my work is attempting to explore this spatial relationship existing among cells.

In my project, the relationships between individual cells or groups of cells are interesting. Our data is presented like the point cloud. It is doubted that if there are any groups existing among these points and if the viruses have neighbors. The methods are mainly categorized into three parts. The first method... (More)
It has been popular to utilize the heuristic methods or the existing methods to discover new findings and explain the mysterious phenomena in other subjects. And it is known that everything in nature relates to each other. In this sense, we could assume that the entire distribution of objects is relative to the locations of individuals. The idea of my work is attempting to explore this spatial relationship existing among cells.

In my project, the relationships between individual cells or groups of cells are interesting. Our data is presented like the point cloud. It is doubted that if there are any groups existing among these points and if the viruses have neighbors. The methods are mainly categorized into three parts. The first method is to integrate the similar objects into groups. Here the similar objects could be the ones that are close to each other. The second method analyzes the degree of closeness between objects and looks for the neighbors of viruses. The last method can be used to draw the border of a point cloud, which seems like constructing the boundary of districts.

Within each method, we carried out the corresponding case studies. Since similar objects can be grouped together, it is interesting to look into the details of each group. Thus we can know which two objects are similar in the same group. Basically, different types of cells in the same group can be checked and studied. In the closeness analysis, we found that some cells are indeed closer to each other. The constructed border could help us know the shape of point clouds.

It can be concluded that the spatial relationship does exist among the cells. Groups of cells can be identified at a large extent. And one certain type of cells could be more attracted by some cells from a local level. However, this study is carried out in a 2D space. Actually, we neglect the real shape of cells which have heights. This could be a more interesting topic in the future. (Less)
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author
Xu, Ruibin LU
supervisor
organization
course
NGEM01 20141
year
type
H2 - Master's Degree (Two Years)
subject
keywords
clustering methods, physical geography and ecosystem analysis, spatial analysis, proximity methods, 2D hull, geomatics
publication/series
Student thesis series INES
report number
327
language
English
id
4779339
date added to LUP
2014-11-18 15:45:09
date last changed
2014-11-18 15:45:09
@misc{4779339,
  abstract     = {Spatial analysis, playing an essential role in data mining, is applied in a considerable number of fields. It is because of its broad applicability that dealing with the interdisciplinary issues is becoming more prevalent. It aims at exploring the underlying patterns of the data.

In this project, we will employ the methodology that we utilize to tackle spatial problems to investigate how the cells distribute in the infected tissue sections and if there are clusters existing among the cells. The cells that are neighboring to the viruses are of interest. The data were provided by the Medetect Company in the form of 2-dimensional point data. 

We firstly adopted two common spatial analysis methods, clustering methods and proximity methods. In addition, a method for constructing a 2-dimensional hull was developed in order to delineate the compartments in tissue sections. A binomial test was conducted to evaluate the results.

It is detectable that the clusters do exist among cells. The immune cells would accumulate around the viruses. We also found different patterns near and far away from viruses. This study implicates that the cells are interactive with each other and thus present the spatial patterns. However, our analyses are restricted in a planar circumstance instead of treating them in 3-dimensional space. For the further study, the spatial analysis could be carried out in three dimensions.},
  author       = {Xu, Ruibin},
  keyword      = {clustering methods,physical geography and ecosystem analysis,spatial analysis,proximity methods,2D hull,geomatics},
  language     = {eng},
  note         = {Student Paper},
  series       = {Student thesis series INES},
  title        = {Spatial analysis for the distribution of cells in tissue sections},
  year         = {2014},
}