Biological Visualization - Microscopy, Flow Cytometery, Electron Microscopy and Image Analysis


BioVis - Biological Visualisation

The BioVis platform of Uppsala University provides you with a unique combination of technology and know-how for visualization of biological samples at the tissue, cell and subcellular level. We specialize in microscopy, electron microscopy, flow cytometry and image analysis. We can offer state of the art electron- confocal and light microscopy, as well as analytical and imaging flow cytometry and cell sorting.

The Medical & Pharmaceutical faculty at Uppsala University supports BioVis financially, thus the user fees can be kept low. The platform is available for all universities, governmental agencies & private companies. Information about users fees can be found here.

With proper training, provided by us, you can get almost complete access to our equipment.

Help us to spread the information that BioVis is available with its service for Uppsala University and beyond. You can download our Brochure here: BioVis Brochure.

Entrance Card System

To get access to BioVis premises you need to have a door-card. Our old Card system (Landstinget i Uppsala Län) is no longer valid. A new card system is established. The new card system does NOT apply for research groups based in Rudbeck Lab, as they have already access. Please contact for more details.

Welcome to the year 2020.

Time for a newsletter from BioVis

Recruitment Flow Cytometry

 Hopefully good news to those looking for a new job position as a research engineer: We would like to recruit someone with experience in Flow Cytometry and cell sorting as a research engineer. The position will be published soon and a link will be added. Position starts 2020/May/01. Meanwhile feel free to contact Dirk Pacholsky.

New instruments

2Photon Microscopy: Our new 2Photon is nearly ready to use. We would like to get it known first by ourself, set up routines, before giving introductions around end of February or March. Feel free to contact Matyas Molnar to get more information

Slide Scanner: We finally can announce that we purchase the SlideScanner AxioScan from ZEISS. Installation will be done in march. We will start to operate the instrument in a full service mode, before opening it for introductions. Dirk Pacholsky will be your contact person.

Selling instruments

Although we are discontinuing our service on the ZEISS Lightsheet microscope Z.1 - the instrument is absolutely fine, intact and functional. We are currently looking for buyers who are interested in this instrument. Matyas Molnar is your contact person here.


We have updated our courses “Methods for Cell analysis”, “Introduction to Image Analysis Software” and “ImageJ”. Our popular Image J course is now a two day course. More information can be found under "Courses & Introductions".

Electron microscopy

Some promotion from our Electron Microscopy node:

Would you like to see what is in your sample before using it for further studies? Negative staining is a simple and quick method to check your biological particles in the electron microscope. We have experience in visualizing isolated exosomes, fibrils, viruses and adjuvanses to mention a few. Please contact the Monika Hodik or Karin Staxäng for further information.


We are currently re-arranging our set up for using IMARIS software. Imaris will be soon available on a Server. This will allow our users to work with larger files, which usually were hard to analyze on a computer station. For the time being, Imaris is available on our Computer-station until we know the Server serves us well. Contact Dirk Pacholsky for more information.

Image/ Data Analysis software at BioVis

We would like to point out that BioVis can help in analyzing your image data using various softwares. We have IMARIS (full package), Huygens on our workstations, a well as Image J, QuPath, and Cell Profiler. We can also refer you to the BioImage Informatics Facility (BIIF) of SciLifeLab, which offers free support in setting up bioimage analysis solutions using ImageJ, CellProfiler, QuPath, KNIME, Ilastik, Python and MATLAB to all researchers in Sweden (20h of free support per Principal Investigator). CellProfiler and KNIME are – next to other applications - especially well-suited for High-Content-Screening data. QuPath is a powerful tool for the analysis of histopathological slides of bigger file sizes (e.g. from slide-scanners, TMAs). Dr. Anna Klemm from BIIF will be one of the teachers at IAS.

For all the Flow Cytometry users we have BD Diva, BC CytExpert (which is a free to use software) and Modfit for Cell Cycle Analysis available.


We are planning to purchase new instrumentsbeginning 2020:

- Super resolution (STED) Microscope: tender will be published end of January

You can find us

Uppsala , Science Park Rudbeck Laboratory, 2nd floor

Dag Hammarskjölds v 20