PhD student in computerized image processing with focus on analysis of tissue samples

Are you interested in developing computational tools and learning strategies for understanding health and disease at the microscopic scale? Would you like to be part of a research team with skilled and friendly colleagues in an international environment? Are you seeking an employer that offers safe and favorable working conditions? If so, check out the following PhD position at Uppsala University.

The Department of Information Technology holds a leading position in both research and education at all levels. We are currently Uppsala University's third largest department, with 350 employees, including 120 teachers and 120 PhD students. Approximately 5,000 undergraduate students take one or more courses at the department each year. You can find more information about us on the Department of Information Technology website.

The project will be led by Professor Carolina Wählby, within the Image Analysis unit of the department’s Vi3 division, working alongside researchers developing numerical and computational methods with a particular focus on deep learning and image analysis. The research is done in close collaboration with the BioImageInformatics Unit of SciLifeLab. SciLifeLab is a national resource of unique technologies and expertise available to life scientists, closely intertwined with a community of researchers in areas such as biomedicine, ecology and evolution. SciLifeLab brings scientists together across traditional boundaries and fosters collaborations with industry, health care, public research organizations and international partners.

More information about being employed as a PhD student at Uppsala University can be found here.

Project description
Digital pathology and detection of cancer based on hematoxylin and eosin (H&E) stained tissue samples has made enormous progress in the past ten years thanks to artificial intelligence, mainly in the form of deep convolutional neural networks. In parallel, functional analysis of tissue samples via novel microscopy techniques and spatial omics has made great leaps in terms of multiplexing capabilities and power to decipher spatial patterns of molecules and cells. They provide insight into cell development, micro-environment interactions, and transformation into diseased states. Yet, combining AI-based analysis of H&E data with spatial omics is only at its very early stages. The purpose of this project is to bridge this gap through development of computational strategies combining digital pathology and function into Functional Pathology, with focus on cancer development.

In this project, the successful candidate will conduct basic research and methodological development to design and implement novel computational models and solutions. A solid theoretical background and hands-on experience in digital image processing and deep learning is essential. A successful candidate should also have a keen interest in collaborating with life scientists and learning more about pathology and tissue analysis. 

The project is financed by the Swedish Research Council.

Duties
The doctoral student will primarily devote their time to graduate education. Other departmental duties of at most 20%, including teaching and administration, may also be included in the employment.

Requirements
Entry requirements for doctoral education are regulated in the Higher Education Ordinance. To meet the general entry requirements for doctoral studies, you must:

• Hold a Master’s degree in computer science, engineering, data sciences, applied mathematics, machine learning, or another related field; or
• Have completed at least 240 credits in higher education, with at least 60 credits at Master’s level including an independent project worth at least 15 credits; or
• Have acquired substantially equivalent knowledge in some other way.

The University may permit an exemption from the general entry requirements for an individual applicant, if there are special grounds (Chapter 7, § 39 of the Higher Education Ordinance). For special entry requirements, please see the subject’s general study plan.

We are looking for candidates with:

• A solid academic background with thorough computational and analytical understanding;
• A strong interest in understanding the nature of existing methods and systems, both in theory and hands-on;
• Proficiency in programming in Python and deep learning frameworks such as PyTorch and TensorFlow;
• Excellent communication skills in oral and written English;
• Creativity, thoroughness, and a structured approach to problem-solving;
• Good collaborative skills, drive, and independence.

Additional qualifications
Experience from working with image data, and in particular microscopy images and life science data is a merit.

Rules governing PhD students are set out in the Higher Education Ordinance chapter 5, §§ 1-7 and in Uppsala University's rules and guidelines.

Application
The application must include:

• A CV;
• Degrees and transcripts with grades (with course name translations in English or Swedish), with the rank/percentile in the graduating class or within a large comparison group indicated in the CV;
• A cover letter (at most one page) containing:
  • a description of your motivation for applying for this position;
  • earliest possible starting date (with reasons if applicable);
  • a brief bullet-point list of three major academic or scientific achievements;
  • (optional) a bullet-point list for additional explanations that the applicant may wish to clarify (e.g., limited experience in a qualification aspect, gaps between degrees, or academic delays) or other remarks, if any.
• A reading sample, e.g., Master’s thesis (or its draft) or another self-produced scientific text. For contributions to joint publications, include a list in the CV with links to papers online, and add the publication with the applicant’s largest contribution as a second reading sample;
• Contact details (names, emails, and telephone numbers) of minimum two references, also specifying the context, duration, and nature of the relationship with the candidate. Reference letters may be provided as supporting document but are not required at the time of the application.

About the employment
The employment is a temporary position according to the Higher Education Ordinance chapter 5 § 7. Scope of employment 100 %. Starting date September 1, 2025 or as agreed. Placement: Uppsala.

For further information about the position, please contact: Carolina Wählby, Professor at the Department of Information Technology, carolina.wahlby@it.uu.se

Please submit your application by April 30, 2025, UFV-PA 2025/946.

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