MSc projects

MSc project

The MSc project is a major part of your masters and the proof of your abilities to future employers.

The project may be performed at TU/e, at another university or research institute, at a hospital or with industry. It is worth 45 or 60 ECs and is concluded by an MSc thesis, a presentation and a defence.

NB: please be aware that you are to have completed all your courses before you can finalize your MSc project. You can no longer take exams once your MSc project has been graded. The externship is the only element that may be performed after the MSc project.


How do I find a project?

You can find a list of projects here, but this list is certainly not exhaustive.

Your mentor can help you. Have a meeting discussing what interests you (and what doesn’t). Do you have a preference for a certain topic, modality or disease? Do you want to stay at TU/e or go to industry or a hospital? Your mentor can give you some suggestions and, once you have studied those and indicated a preference, give you contact information for the institute of your choice. For external projects, please do not contact a large number of people at once.

You are of course not bound to the suggestions of your mentor. If you find a project yourself (via the internet or a fellow student or whatever), however, do discuss with your mentor whether the institute and project are suitable.

NB: ME students generally do their project at a hospital, but at the very least an expert with a clinical task should be involved.

How do I register my MSc project?

You need to officially register your project. There is a form to be filled in and signed by your supervisors. Before signing, your supervisor will want to see a brief description of your project (half a page is sufficient). Please note that this form is to be submitted at the Education Office before the start of your project.

What are the elements I am judged on?

Your achievements will be judged by a small committee of at least three members of staff, of which one is from another group in the Department. Additionally, other supervisors may be involved in the evaluation.

Basically, we judge how well you can perform a true research project, regarding all aspects involved. This includes independence, practical and experimental skills, creativity and innovative elements of the work, critical analysis of the results, structure and clarity of thesis, understanding of problem and methods, presentation and defence.

What is the purpose of the midway presentation?

When you are roughly half way through your project, you will present your work to the IMAG/e group and the other master students at a Group Meeting. This serves to let others know what you are working on, but it is also an opportunity for you to get feedback and input. The presentation should describe the problem you work on, an overview of what you have done so far and briefly what you plan to do in the second half of the project. If you want, you can include some discussion topics (questions or problems) that the group may help you with. The midway is not an evaluation, it does not count towards the final grade for your project.

Erica will contact you in due time to plan a date for your midway. The presentation is scheduled for about 20 minutes.

In which format should the MSc thesis be?

The core part of your MSc thesis will be formed by a scientific paper, describing your research project. You will find this forces you to select which results are relevant for your thesis, to present results in a summarised way and to write in a concise style.

In addition, the thesis will contain a Background section, which serves to introduce any clinical and/or technological elements not covered in the paper. In a scientific paper you will leave out what is considered common knowledge for the readers. Your thesis, on the other hand, should be understandable for a fellow student or researcher in the BIM cluster and they will not be familiar with specialist methods and specific treatments. To give some examples, you do not have to explain how a neural network operates or how MR imaging functions, but you should describe how radiotherapy treatment plans are evaluated, how CEST imaging works or how an advanced type of deep learning framework operates.

You are free to include a Literature review section if you have done an extensive review, more extensive than is common in a RelevantLiterature section in a scientific paper. The thesis can end with appendices, for instance, to include additional results, to present a mathematical derivation or proof and/or to present some work that took a substantial part of your time but did not end up in your thesis.

Summarising, the elements of your MSc thesis are:

  • Background section
  • Literature review section (optional)
  • Scientific paper
  • Appendices (optional)

The guidelines of the department contain additional information on MSc theses.

We ask you to use the scientific paper format of the IEEE Transactions on Medical Imaging journal for your scientific paper. You can find the specifications here. Using this double-column format, the scientific paper part of your thesis is to be 10-12 pages in length, with up to two additional pages for references. That may not sound like much, but this format is very dense. You are free to format the other elements of your thesis differently.

How about my final presentation?

When you are a few months from finishing your project, you should discuss with your TU/e supervisor whether he/she thinks you will indeed finalize your work according to plan. If so, your supervisor will decide on a committee and determine a suitable date for your presentation. You are to apply for the assessment of your MSc project (see here), which is only possible when you have completed all your courses and your study programme meets the requirements of the Department. You will obtain a form to apply for approval of your MSc exam by the Exam Committee. This form needs to be signed by the chairman of the EC numerous weeks in advance of your presentation (usually four weeks, but check the study guide!). So start early, because we will also need some time to compose an evaluation committee for you.

Also contact the secretary (, as she will arrange the room for your presentation and sends the form to the chairman of the committee. She can help you out with many of the logistics.

You are to make sure your report is distributed to the committee members, either in digital or paper form (whatever they prefer). You are to upload your report for the Department, but know that your committee members cannot access that database, so you need to provide them with a copy.

Your presentation is to last at most 20 minutes and is in public, meaning you can ask friends and family to attend, if you like. Afterwards, there is some time for questions from the audience. The next and final part is the defence.

What does the defence entail?

You will have a discussion about your work with the committee. This is a closed session, only you and the committee. The discussion takes around 45 minutes, to at most an hour. The committee will then ask you to leave the room and determine your grade, while you nervously pace the halls. As soon as consensus has been reached, the committee will call you back, inform you of your grade and give you some feedback on how they came to this grade. Then you celebrate and either leave to do your externship or go off into the real world.

When I am finished, what can I take with me and what do I leave behind?

Be aware that you cannot take anything with you, other than the report you wrote, unless otherwise agreed with your supervisor or responsible faculty member. That applies to code, data, and such. We will likely allow you to keep a large part of what you created during your project, but perhaps not all and you do need permission. When you have done a project with an external party (company, hospital, other research group), this is particularly important!

Your supervisor will discuss with you which data, code and results they would like you to transfer. You will hear with which parts to gather, in which format and where to store them.

And most importantly, CLEAN UP! Remove everything other than what your supervisor asks you to archive. Future students will appreciate the storage space.

Please also read this document !