Positions in Biomedical Image Analysis

Below is a list of possible research themes that could be taken as PhD subject areas. These are a guide of my research interests in which the common thread is the analysis of challenging 2D and 3D data sets, with a preference towards Biomedical topics. If you have your own ideas do let me know as there is always flexibility.
For PhD opportunities, you will have to have finished a first degree and preferably an MSc (or equivalent) on Computer Science, Engineering or Physics, strong engineering / computational skills and experience with Matlab is a plus.

Previous knowledge on Medicine and Biology is not necessary, but having an interest is important as the understanding of where the data come from can help the coding and analysis of it.

Informal enquiries should be directed to Dr Constantino Carlos Reyes-Aldasoro (reyes@city.ac.uk) and should include a copy of academic transcripts.

• Neutrophil analysis
  
  Neutrophil migration in zebrafish larvae is increasingly used as a model to study the response of these leukocytes to different determinants of the cellular inflammatory response. However, it remains challenging to extract comprehensive information describing the behaviour of neutrophils from the multi-dimensional data sets acquired with widefield or confocal microscopes.
  This PhD project will focus on the development of image analysis algorithms to extract quantitative information, which will then be used to interpret the behaviour of neutrophils as observed in zebrafish. The project will build on a previously developed a series of tools for the segmentation and tracking of neutrophils in zebrafish (www.phagosight.org), which were developed in collaboration with the University of Sheffield who will provide the expertise in zebrafish and neutrophils. PhagoSight contains algorithms for the segmentation and tracking aspects of neutrophils in zebrafish areas to be explored are the shape of the cells, their interaction and the position relationship with the anatomy.


• Analysis of the movement of small crustaceans in microfluidic environments
  
  This project is a collaboration with the University RMIT in Australia. Through the observation of small crustaceans (Artemia Franciscana) in microfluidic environments is possible to analyse conditions that flow through the environment and the effect on the animals, and from there it is possible to extrapolate the situation in larger ecosystems, like marine environments, which are more difficult to observe. The basis of this project is to develop algorithms to analyse the movement of the crustaceans and to figure if it is possible to develop an improved observation setting.


• Analysis of Tissue stained through Immunohistochemistry
  
  Abnormal growth of cells inside the brain is relatively rare, but is serious and life threatening when it leads to brain tumours. Recent research has shown that certain features of certain tumours are probably important in predicting their response to treatment, but the relationship between the different features is so complicated that this information cannot yet be used to help patients. This multidisciplinary proposal will investigate in detail how various characteristics of brain tumours impact on patient outcome. The aims of this project are to obtain quantitative measurements from the images of tumour specimens and evaluate which measurements, or sets of measurements, correlate best with patient outcomes such as life expectancy and response to treatment. This project requires programming image analysis algorithms in Matlab to segment the different cells in tumours stained by immunohistochemical techniques.


• Analysis of Bees' beaviour
  
  This project is a collaboration with the laboratory of social insects of the University of Sussex (http://www.sussex.ac.uk/lasi). The aims of this project are to extract information regarding the complex behaviour of bees from their movements from videos, in order to do that it is necessary to develop segmentation and tracking algorithms. This is a very challenging problem as the images of the bees are complex and difficult to analysed through algorithms.


• Analysis of Ants' beaviour
  
  This project is a collaboration with the laboratory of social insects of the University of Sussex (http://www.sussex.ac.uk/lasi). The aims of this project are to extract information regarding the complex behaviour of ants from their movements from videos, in order to do that it is necessary to develop segmentation and tracking algorithms. This is a challenging problem as the images of the bees are complex and difficult to analysed through algorithms.


• Analysis of 3D sand data sets
  
  This project is a collaboration with Civil Engineering at City. Large part of world’s seabed is covered with shelly carbonate sands, a type of sand formed by skeleton bodies and shells of small organisms. Understanding the behaviour of this sand is critical for the design of offshore structures. This interdisciplinary project combines acquisition with a 4D synchrotron x-ray and sophisticated processing and visualisation analysis to characterise the mechanical deformation of the individual shelly grains to inform modelling and construction practices. The image shows a single shell extracted from the sand sample.



• Analysis of 3D Palates for Phonetics
  
  This project is a collaboration with the School of Health at City and is being currently funded for 3 years by the Leverhulme Trust. This project investigates to what extent asymmetries in the articulation of speech are due to anatomical asymmetries in palate shape of speakers. For this purpose a stone cast of a speaker’s palate was made and scanned by means of a CT scanner. These images were used to make a three-dimensional reconstruction of the speaker’s palate. Electrodes placed on the palate enable accurate measurement of depth differences between the left and right side of the palate. This research has various applications in speech therapy.

City, University of London regularly provides a series of competitive scholarships, to which you can apply for these projects. These scholarships are highly competitive so do not assume that you can get one of them, I suggest that you search for alternative sources of funding such as British Council or national funding bodies.

To have more information regarding the funding opportunities, please visit this page, and explore the options. Some of these opportunities ONLY cover the UK/EU fees so, if you are not an EU national, it will be necessary that you can cover the difference between the UK/EU and the international fees.

Students from European Universities can join City in Erasmus exchanges, normally towards the endo of a Master's degree and they can complete their research theses within our premises. Please contact me if you are interested.

Most universities recognise only two visiting schemes: Visiting Scholar for post-doc level or higher, and Visiting Student. Unless there is an agreement between universities, visiting student will need to need to pay fees. If you can find funding for this, you are welcome to come during the summer (or any other time of the year). We have short projects that may be of interest for students of Computer Science and Engineering with interests on Image Processing. You will need to be in the last year of a degree, have some experience of signal/image processing, and very good use of Matlab.

I cannot offer any funding so only contact me if you can sort your own funding for travel and visa arrangements.

For Postdoctoral positions, will be announced here, watcht this space.