Skip to main content

LUP Student Papers

LUND UNIVERSITY LIBRARIES

Biomedical image analysis with artificial intelligence

Arvidsson, Malou (2021) BINP51 20201
Degree Projects in Bioinformatics
Popular Abstract
Cell Death Detection in Images

What if we could kill cancer cells? The fact is that we already can, at least to some extent. Many cancer treatments targets cancer cells and kill them by causing them to commit suicide. To be able to do this even better, and minimize adverse effects, information about the biological regulation behind cell death needs to be known, and far from everything has been discovered. Apart from cancer treatments, cell death plays a big role in many other diseases, e.g., Alzheimer’s disease and stroke. Learning more about cell death can help in the discovery of treatments and cures for all these diseases.

Every living thing is built by cells, and the cells needs to die to make room for newer cells, remove damaged... (More)
Cell Death Detection in Images

What if we could kill cancer cells? The fact is that we already can, at least to some extent. Many cancer treatments targets cancer cells and kill them by causing them to commit suicide. To be able to do this even better, and minimize adverse effects, information about the biological regulation behind cell death needs to be known, and far from everything has been discovered. Apart from cancer treatments, cell death plays a big role in many other diseases, e.g., Alzheimer’s disease and stroke. Learning more about cell death can help in the discovery of treatments and cures for all these diseases.

Every living thing is built by cells, and the cells needs to die to make room for newer cells, remove damaged cells or prevent the spread of cells that are mutated and could become cancer cells. A cell consists of many small parts (organelles) and a core called nucleus in which the DNA is stored. A dying cell goes through changes in appearance such as increased or decreased cell size or changes in its shape. The nucleus of the cell may also increase or decrease in size and other organelles within the cell may also change during the cell death process. These changes can be visualized in a microscope by using specific colour stains for the cells.

The human genome consists of around 20 000 genes. Each gene has one or several functions and some of these genes’ functions are involved in cell death. Mutations in these genes thus change the controlled cell death process. To identify the genes which are involved in controlling cell death, one can make use of methods which disable genes one at a time and then look for cell death changes in a microscope

In this project, I have worked with a large microscopy image set, for which all human genes have been disabled, one at a time, before staining them with cell death-specific markers. The image set consists of millions of images, - too many to look at and analyse manually. To analyse all these images, automated processes are required. I have therefore used a machine learning method, to locate all cell objects in the images, count them and measure the size of them in a few seconds per image.
The final product of the project was a program to predict, and evaluate many images in an automated process, which can be applied in batches to the whole image set in parallel, so that the analysis is sped up.

The program was tested on 30 000 images, half of them were images of cells known to be in a cell death process. The analysis of these images showed that large differences could be detected between dying cells and healthy cells, meaning that the program is now ready to be used on the entire dataset to gain insights about which genes are controlling cell death processes.


Master’s Degree Project in Bioinformatics 45 credits 2021
Department of Biology, Lund University

Advisor: Sonja Aits
Department of Experimental Medical Science, Lund University (Less)
Please use this url to cite or link to this publication:
author
Arvidsson, Malou
supervisor
organization
course
BINP51 20201
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
9075474
date added to LUP
2022-02-16 16:41:27
date last changed
2022-02-16 16:41:27
@misc{9075474,
  author       = {{Arvidsson, Malou}},
  language     = {{eng}},
  note         = {{Student Paper}},
  title        = {{Biomedical image analysis with artificial intelligence}},
  year         = {{2021}},
}