Course in confocal microscopy

Last changed: 10 February 2022

Confocal microscopy

 (7 credits)

November 3d - December 10th, 2014


2014.12.10 9:00-12:00 Seminar 4 (Report), BioCenter C-212 (2d, ground floor)

The last homework (Report)

Seminar 3 (Softwares) original keynote fileAlyona Minina

Lecture 10 (ImageJ) example files, Panagiotis  Moschou, Department of Plant Biology, SLU

Lecture 9 (ZEN Blue), Eric Muren, Carl Zeiss AB

 Lecture 8 (ZEN Black),  Dirk Pacholsky, BioVis, UU

Homework for the 27th

Hands-on 2PM, LightSheet, SIM. Schedule

 Lecture 7 (LightSheet microcsopy), Dirk Pacholsky, BioVis, UU

Lecture 6 (Multiphoton mciroscopy),  Matyas Molnar, BioVis, UU

Lecture 5 (SHG),  Matyas Molnar, BioVis, UU

Homework for the 25th

Practical part using Zeiss 780. Schedule

Seminar 2 (planning the practical part), Alyona Minina

Lecture 4 file was sent via e-mail (High Resolution microscopy), Hans Blom

Lecture 3, version with text (CARS microscopy), Juris Kiskis

Seminar 1 (Basics of confocal microscopy), Alyona Minina

Lecture 2 (Basics of confocal microscopy), Alyona Minina

Lecture 1 (Basics of light microscopy), Alyona Minina


Useful stuff  

BioCenter Confocal Platform

BioCenter Imaging Platform  instructions for Mac and Windows users


Open-source softwares:

ImageJ and Fiji (ImageJ+plugins)



Colocalization quantification:

Colocalization quantification & noise signal

Colocalization Pearsons vs Manders

Colocalization quantification in plant cells


FRET quantification:

Quantification of FRET


FRAP quantification:

Quantification of FRAP


Fluorescence intenisty qunatification:

Quantification of fluorescence intensity


Publishing digital images:

Figure manipulation: assesing what is acceptable. JCB

Manipulation and misconduct in handling of image data. Plant Cell



Here you can find the syllabus  and  preliminary schedule


Thanks to the rapid development of technology the fancy confocal microscopy is now available for every day use, this opens completely new horizons for both great discoveries and missing controls. The aim of this course is to provide students with a solid theoretical background essential for designing their experiments, introduce them to the  most common softwares and also to give students an opportunity to have a hands-on experience with confocal microscopes available at the BioCenter and SciLifeLab, UU. Students will also meet experts from SciLifeLab, Stockholm and Chalmers to learn about other microscopy technologies available in Sweden.





To register for the course send an e-mail to: alena.minina @

Deadline for registration: October 20th 2014

All lectures are open, registration is required only to attend the practical part of the course





Alyona Minina, Department of Plant Biology, SLU

Hans Blom, SciLifeLab, KTH

Juris Kiskis, Chalmers University of Technology

Dirk Pacholsky, BioVis, UU

Matyas Molnar, BioVis, UU

Eric Muren, Carl Zeiss AB

Panagiotis  Moschou, Department of Plant Biology, SLU


Participants (max 20 students)

  1. Salim Hossain Reza, Department of Plant Biology, SLU<
  2. Sultana Jahan, Department of Plant Biology, SLU
  3. Jing Lu, Department of Food Science, SLU
  4. Maria Karlsson, Food Science, SLU
  5. Maria Leonor Segurado Gouveia, Department of Immunology, Genetics and Pathology, UU
  6. Rita Batista, Department of Plant Biology, SLU
  7. Anna Carlson, Department of Plant Biology, SLU
  8.  Shirin Akhter, Department of Plant Biology, SLU
  9. Daniel Johansson, Department of Food Science, SLU
  10. Masud Parvage, Deaprtment of Soil and Environment, SLU
  11. Tania Tajrin, Department of Ecology and Genetics, Evolutionary Biology, UU
  12. Ylva Sjunnesson, Department of Clinical Sciences, SLU
  13. Daniel Uddenberg, Department of Physiological Botany, UU
  14. Xue Zhao, Department of Food Science, SLU
  15. Eva Hellmén, Department of Clinical Sciences, SLU
  16. Clément Lafon-Placette, Department of Plant Biology, SLU
  17. Mohammad Jaber Alipour, SLU
  18. Panisara Kunkitti, SLU