Welcome to the LCI Facility

Microscopy course 17.01-09.02/2017

Do you feel that your sample or your settings could be improved? Are you unsure of your microscopy skills? This course is perfect for you! Learn all the fundamentals of microscopy in details: what is resolution? How to choose the pixel size on a confocal? Which objective is most appropriate for this experiment? How to get rid of tissue autofluorescence? How to handle images for publication or get relevant statistics?

Microscopy: improve your imaging skills - from sample preparation to image analysis (#2870)

Full course including all lectures, workshops and group work. Includes a workshop where you get personalized feedback using your own sample!

Microscopy: improve your imaging skills (#2871)

Reduced course including all lectures and group work


Beautiful images acquired at the LCI facility

Mouse mammary gland LCI

About the facility

The Live Cell Imaging Facility is a light microscopy facility at the Department of BioNut in Huddinge

The Live Cell Imaging facility was started in 2009. Since then the facility has grown to include 6 high-end microscopes, 3 experienced staff and a high image analysis capability. About 70 researchers actively use the equipement at the LCI facility.

Together our microscopes allow researchers to perform conventional and high throughput confocal and widefield microscopy, fast confocal microscopy (resonance scanner and spinning disk), Fluorescence LifeTime Imaging (FLIM), multiphoton microscopy, spectral imaging and super resolution microscopy (TIRF and STORM). Additionally the NIS-Element and Imaris software are available for manual or fully automated or semi-automated image processing and analysis.

The Live Cell Imaging facility is grateful to the founding agencies that allowed its development: Vetenskapsrådet, the Knut and Alice Wallenberg Foundation, the Center for Biosciences/CIMED and the KI fund for core facilities.

Today the LCI facility is proud of being part of the The Jonasson Centre for Medical Imaging, the network of Nikon Center of Excellence, as well as being member of several international imaging networks (Swedish Bioimaging Network, European Light Microscopy Initiative).

Jonasson Centre for Medical Imaging and Nikon Center of Excellence

Inauguration of Nikon Center of Excellence at BioNut

The Jonasson Centre for Medical Imaging was established in 2014 after a donation from Kerstin och Rune Jonasson. The overall aim of the Centre is for healthcare, technology and research in the region to become world-leading within image function.

The LCI facility is happy to host 2 high-end microscopes that are part of the Jonasson Centre: The Pegasus and Orion systems allow researchers to perform confocal imaging and super-resolution microscopy.

In 2014, the LCI facility was awarded the prestigious Nikon Center of Excellence label. The facility became one of only 8 Centers of Excellence in Europe, 15 in the world. The Center officialises a tripartite collaboration between the Live Cell Imaging facility at the Karolinska Institute in Huddinge, the School of Technology and Health at the Royal School of Technology (KTH) in Huddinge and Nikon Instruments Europe.

This collaboration includes sharing equipment, resources and knowledge in order to offer the best possible service to the users of the LCI facility and contribute to the development of the Nikon confocals and software. The Nikon Center of Excellence comprises the 5 state-of-the-art Nikon confocals present at the LCI facility.

Equipment and software

The LCI Facility is equipped with 6 microscopes, 4 point scanning confocals, a widefield/spinning disk microscope and a  2-photon microscope.


Would you like to get trained by us but to use a microscope at your own department? In this case our facility offers two types of service:

Training at the LCI facility

Get trained on your own microscope

We also run a yearly course on microscopy. This is for experienced microscopists to learn more.

Practical information


Fees at the LCI Unit

The Live Cell Imaging facility is open to all researchers. Prices are listed below.

Users pay an entry fee once. This includes training as well as help with sample preparation, experimental design and image analysis. Additionally, users pay the usage fee, every year, 3 or 6 months depending on the length of their project.

The entry fee for the Nikon confocals gives access to 4 confocals (Tweety, Pegasus, Dragon and Orion). The entry fee for the Nikon widefield systems gives access to TIRF on Orion and TIRF, widefield or spinning disk on Victor. Finally there is an entry fee for the Zeiss confocal (Zeus) which gives access to one confocal with a multiphoton option. If one user has paid for one of the entry fees then needs to start using a different system, the new entry fee is cheaper (see table below).

1. Entry fee per user and per microscope or software (includes advanced training and expert assistance)

Entry fee for first training 12.000 SEK
Entry fee for subsequent training 9.000 SEK
Entry fee for Imaris or NIS (offline PC only) 5.000 SEK

2. Usage fee
There is no additional fee per hour. The usage fee is the same regardless on the number of microscopes you use (after training).

  12 months 6 months 3 months
Offline software only 4.000 SEK 2.500 SEK 1.500 SEK
Microscopes and offlines 15.000 SEK 9.000 SEK

6.000 SEK

For non academic users the yearly fee is 30,000 SEK


Registration and booking

Booking at LCI Unit

Fee form

Booking (log-in required)


Laser safety

Laser safety at the LCI unit
Lasers at the LCI facility microscopes fire visible or invisible light.  Invisible lasers are the 405 nm laser and the multiphoton laser.
Never look down the eyepiece when the system is scanning, even if you do not see any light!
Laser safety at the LCI facility



Guidelines LCI Unit

The LCI facility guidelines must be followed by all users.

Selected publications

Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos.
Petropoulos S, Edsgärd D, Reinius B, Deng Q, Panula S, Codeluppi S, et al
Cell 2016 May;165(4):1012-26
Super-resolution microscopy reveals γ-secretase at both sides of the neuronal synapse.
Schedin-Weiss S, Caesar I, Winblad B, Blom H, Tjernberg L
Acta Neuropathol Commun 2016 Mar;4():29
Xeno-Free and Defined Human Embryonic Stem Cell-Derived Retinal Pigment Epithelial Cells Functionally Integrate in a Large-Eyed Preclinical Model.
Plaza Reyes A, Petrus-Reurer S, Antonsson L, Stenfelt S, Bartuma H, Panula S, et al
Stem Cell Reports 2016 Jan;6(1):9-17
VAMP8-dependent fusion of recycling endosomes with the plasma membrane facilitates T lymphocyte cytotoxicity.
Marshall M, Pattu V, Halimani M, Maier-Peuschel M, Müller M, Becherer U, et al
J. Cell Biol. 2015 Jul;210(1):135-51
Tissue-infiltrating neutrophils represent the main source of IL-23 in the colon of patients with IBD.
Kvedaraite E, Lourda M, Ideström M, Chen P, Olsson-Åkefeldt S, Forkel M, et al
Gut 2016 Oct;65(10):1632-41
Mitochondrial Polyadenylation Is a One-Step Process Required for mRNA Integrity and tRNA Maturation.
Bratic A, Clemente P, Calvo-Garrido J, Maffezzini C, Felser A, Wibom R, et al
PLoS Genet. 2016 May;12(5):e1006028
Early B cell factor 1 regulates adipocyte morphology and lipolysis in white adipose tissue.
Gao H, Mejhert N, Fretz J, Arner E, Lorente-Cebrián S, Ehrlund A, et al
Cell Metab. 2014 Jun;19(6):981-92
The atypical ubiquitin ligase RNF31 stabilizes estrogen receptor α and modulates estrogen-stimulated breast cancer cell proliferation.
Zhu J, Zhao C, Kharman-Biz A, Zhuang T, Jonsson P, Liang N, et al
Oncogene 2014 Aug;33(34):4340-51
Verification of cell viability in bioengineered tissues and organs before clinical transplantation.
Jungebluth P, Haag J, Lim M, Lemon G, Sjöqvist S, Gustafsson Y, et al
Biomaterials 2013 May;34(16):4057-67
Intracellular uptake and toxicity of Ag and CuO nanoparticles: a comparison between nanoparticles and their corresponding metal ions.
Cronholm P, Karlsson H, Hedberg J, Lowe T, Winnberg L, Elihn K, et al
Small 2013 Apr;9(7):970-82
Molecular networks of DYX1C1 gene show connection to neuronal migration genes and cytoskeletal proteins.
Tammimies K, Vitezic M, Matsson H, Le Guyader S, Bürglin T, Ohman T, et al
Biol. Psychiatry 2013 Mar;73(6):583-90



Research engineer

Sylvie Le Guyader

Phone: 08-524 811 07
Organizational unit: Department of Biosciences and Nutrition (BioNut), H2
E-mail: Sylvie.Le.Guyader@ki.se

LCI room: +46 (0) 8 5248 1172
mobile: +46 (0) 73 733 5008

Microscopy Engineer

Project coordinator

Gabriela Imreh

Phone: 08-524 811 75
Organizational unit: Strömblad
E-mail: Gabriela.Imreh@ki.se

Microscopy Engineer

Assistant Professor

Tobias Nyberg

Phone: +46-8-790-4865

E-mail: tobias.nyberg@sth.kth.se



Staffan Strömblad

Phone: 08-524 811 22
Organizational unit: Strömblad
E-mail: Staffan.Stromblad@ki.se

Live Cell Imaging facility
Dept. of Biosciences and Nutrition
Karolinska Institutet
141 83 Huddinge, Sweden

(Visit: Novum, Hälsovägen 7, G lift to floor 6)

How to find the LCI Facility

Way to LCI unit
Live Cell Imaging Facility
Karolinska Institutet
Dept. of Biosciences and Nutrition
Hälsovägen 7, G lift, floor 6
141 83 Huddinge, Sweden

Public Transport:
From T-Centralen, take the commuter train (Pendeltåg, indicated by a blue J) towards Tumba or Södertälje C
Get off at the Flemingsberg station (NOT Huddinge) and walk towards the front of the train.
Follow the crowd towards the hospital up a small escalator then to the right then up a long escalator.
At the top of the escalator, walk straight ahead but very slightly to the right, pass the ‘door’ sculpture then below a building and across a small bridge.
Walk straight ahead for about 200 m and you will see a sign Novum above the path.
By the sign, walk into the building to your right.
At the end of the hall on the left is the G lift.
Go up to the 6th floor then to the glass door just next to the lift.

Useful Links

Looking for a microscopy job? Wondering which analysis software is best for your images or where to find answers to your microscopy questions? Click here!

Teaching material & events


LCI events

Datum Event
24 Oct 2016 - 13:00 Crest spinning disk by NIKON
08 Nov 2016 - 09:30 Primo micropatterning device by Alveole

Bleed through video

How to identify and avoid bleed through between fluorophores

Basics in Nikon NIS-Elements for confocal

Basics in Nikon NIS-Elements for confocal

How to find your sample without bleaching it

How to find your sample without bleaching it

Bit depth, saturation and underexposure

Bit depth, saturation and underexposure

Introduction to image analysis using NIS Element

Introduction to image analysis using NIS Element