Competence Center for Hidden Biodiversity

The Competence Center for Hidden Diversity is built on collaborations between research groups at the Evolutionary Biology Center at Uppsala University. We share an interest in the hidden majority of eukaryotes that remain undescribed and understudied because of their cryptic life cycles in natural habitats like water and soil, also including parasites of other eukaryotes. These organisms are part of often complex communities or live as members of organismal consortia such as lichens and corals. In the competence center we study the diversity in forms, species and life strategies of eukaryotic microorganisms in pure cultures as well as complex natural samples. We plan to do this by combining single cell genomics, microfluidics and advanced microscopy for synchronized capture of genomes and morphology from hitherto unknown organisms. We develop tools and workflows that allow us to describe and better understand the majority of life on earth.


Anna Rosling
Veera Tuovinen Nogerius
Lars Behrendt
Fabien Burki

Microscope image

Confocal microscopy

In 2022, a generous donation in the name of Birgitta Sintring, allowed us to acquire a confocal microscope to the Center. The equipment is also available for users outside the core projects of the Competence Center. We provide training and open the instrument to external users for a fee that is meant to cover our cost of keeping skilled personnel that maintain the microscope and develop protocols and practice. You can find more information on the confocal microscope and user fees below.


We ask that you acknowledge the donation in Birgitta Sintrings name when publishing images and data generated using the confocal microscope. Further we ask that you send us a link to your published work so that we can compile a list of publications that have benefited from the Center. 

Confocal microscope specification

Inverted Leica Stellaris 5 confocal laser scanning microscope

  • Tunable pulsed white light laser, capable of providing up to eight (8) excitation lines simultaneously within the spectral range of approximately 488-680 nm
  • 405 laser, 448 laser
  • 5 fully tunable internal detection channels (Power HyD D), emission detection up to 850 nm
  • 8 kHz tandem scanner, switchable between resonant and non-resonant scanning
  • Objectives:
    • Plan apochromatic objective 10x/0.40
    • Plan apochromatic 20x/0.75
    • Plan apochromatic 40x/1.25 GLYC with motorized correction collar
    • Plan apochromatic 63x/1.40 OIL
    • DIC functionality for 40x and 63x objectives
  • TauSense, a set of tools based on fluorescence lifetime information, provides an additional contrast, improved image quality and separation of spectrally overlapping fluorophores.
  • LIGHTNING which allows adaptive image deconvolution and maximum resolution

How to become a user of Leica Stellaris system

In order to use the microscope service, every user must attend an introductory seminar “Basic education” at BioVis Facility, UU. The seminar consists of introduction to fluorescence and confocal microscopy. The introduction is given once per month given that there are four attendants, for more information about dates and prices please check here.

If you are interested in becoming a user, please contact Veera Tuovinen Nogerius or Johanna Liljestrand-Rönn.

Price list for Leica Stellaris system for external users (2023)

(Note that the prices will be regularly updated)

Introductory training to the microscope: 2200 kr

  • Includes hands-on training on the microscope
  • After the introduction, 700kr/hr for full support until the user is skilled enough to use the microscope on their own. 

Independent use 350kr/hr up to 40 hrs

  • After 40 hrs 100kr/hr 

Last modified: 2023-03-07