Courses

The course Methods for Cell Analysis has been organised by BioVis since 2007. It is a 3.5 credit point course for postgraduate students, post-docs and research engineers who wants to learn more about Light Microscopy, Flow Cytometry and Electron Microscopy. The course is based on a lecture series and practical hands on sessions. Lectures will cover e.g. theory of fluorescence, its application in various light microscopy techniques and flow cytometry. Electron microscopy and latest technical achievements like super resolution are covered as well. The practical hands-on sessions include resources found at BioVis like laser scanning and two photon microscopy, flow cytometry and cell sorting, electron microscopy. For more information please contact Matyas.Molnar@igp.uu.se and see a schedule example xlsx, 119 kB. from an older semester.

Methods for Cell Analysis Spring (2026): Click here for application

Methods for Cell Analysis Autumn (2026): Click here for application

Some reviews from previous students about the course:

_{"This is definitely a must for everyone who wants to further expand their knowledge regarding microscopy methods available in-house to further enrich their research. I will definitely recommend it. "}

_{"In general, the lectures were very well organized and the outcome of the courses are fruitful. Especially the first three lectures that Matyas gave, his teaching style and technique make students really want to learn more."}

_{"Absolutely great hands-on sessions! I have learned so much and many things became clear from the lectures irl. So great we could also handle and try out the different techniques and apply with your excellent guidance what to do, but at the same time also had time to think ourselves."}

_{"All of the teachers are fantastic, and I strongly recommend this course to PhD students who are just starting out."}

_{"I really enjoyed the course. I think this was probably the best course I have taken from all the PhD courses. Thanks to all the teachers and especially to Matyas for explaining the concepts so well, that I actually understood the (simplified) physics behind it."}

_{"Very nice course! Hope all my phd courses could be as nice as MCA. Thanks so much."}

_{"I will recommend this course to my colleague. It is the first time I feel like I finally understand the microscope (even though I have studied this before). Great course!"}

_{"Great course, I learned a lot, very good and passionate teachers."}

The course, Introduction to Image Analysis Software (IAS, PhD Course 1.5hp) is intended to help scientists become more comfortable with image analysis. The IAS course is suitable for those with minimal image analysis experience and also suitable for those wishing to expand their knowledge and take it farther. There are two main goals - i) understanding the fundamentals of image analysis and ii) learning how to apply this knowledge using available software. Initially working with ImageJ, the most popular scientific software, and learning how to create macros to automate analysis. The course ends with the participants, working in groups, presenting their solution to a problem they are interested in. Cell Profiler, QuPath, Imaris, Napari and the deconvolution with Huygens will also be demonstrated during the course.

Course Structure: For 2026, the lecture material will be presented in afternoon sessions 13-16:30 - with learning spaced out over three weeks and a total of nine course days.

For more information contact: ross.smith@igp.uu.se

IAS Course Spring (2026): Click here for application

IAS Course Autumn (2026): Click here for application

Image Analysis

Image acquisition is not the final step in your experiment, journals increasingly want measurements and a full description of image analysis and processing; the number of GFP positive cells, colocalization, the size of cells etc. BioVis now offers consultation to help individuals and research groups with the challenges of image processing and image analysis. A bookable calendar will be available on the iLabs site where you can book a time and work with BioVis staff to address your project's needs.

Get help in such areas as:

• Introduction to Image Analysis Software (ImageJ, QuPath, Napari, IMARIS)
• Guidance on how to design an analysis pipeline
• Writing image analysis scripts (ImageJ, Python)
• Deconvolution using Huygens (for more on this, see below)

Please direct any questions to ross.smith@igp.uu.se

Image Deconvolution using Huygens

Deconvolution improves the quality of images (resolution and noise) based on the known optical properties of the microscope and the fluorophores. The gain can be substantial, especially with widefield images when much of the out of focus blur is removed. Deconvolution also substantially improves confocal, multiphoton images and STED images.

Improve your images - legitimately. The quality of images can be substantially improved using the known optics of the microscope and the fluorophore’s spectra. The result is an increase in resolution and a reduction in noise, which improves the appearance and improves subsequent quantitation. We use the commercial software Huygens (SVI) running on a powerful computer. After training you can book and use Huygens on our computer.