The LCI core facility is now a member of Eurobioimaging!

Good news! The LCI facility is now part of the Swedish Eurobioimaging node! 🙂

This means that you can apply for funds to come and get trained, do some job shadowing or image at the LCI core facility!

The Swedish Eurobioimaging node is even partner in special European funding programs for Agroecology, and Cancer research.

We are looking forward to welcoming you to our facility! 🙂


A few spots left at the LCI microscopy course 29/01-16/02 2024

There are a few spots left for the LCI core facility light microscopy course (29 Jan – 17 Feb 2024): Microscopy: improve your imaging skills – from sample preparation to image analysis’ (6 credits).

This course is completely unique in that it is a highly hands-on, but your hands will be on your own microscope and own sample. The course runs completely remotely! 😊

  • To see how the course can help your microscopy project, check the course webpage. Look at the course schedule 2024 and the alumni testimonies!
  • Also check the course syllabus to see the eligibility criteria. Also read what you will learn in the Course content and Intended Learning Outcomes sections.
  • If you cannot apply to the course, you can anyway follow any of the lectures (in blue on the schedule) as they will be publicly broadcasted live on Zoom and accessible to anyone without registration. The schedule and zoom link are available on the course page.

The purpose of the LCI facility microscopy course is to provide PhD students, researchers and core facility staff who have some prior experience of microscopy with enough theoretical and practical knowledge about their OWN sample and their OWN microscope, to enable them to:

1) assess and improve their sample so that it becomes suitable for data extraction from fluorescence images,

2) make best use of the hardware available in their lab/facility,

3) fully understand the acquisition parameters they need to set in their own microscope software,

4) design their experiment from scientific question to image analysis using a strong knowledge base.

The aim is to provide you with tools to acquire on ANY wide field, confocal or light sheet microscope, images of your samples that reliably answer your scientific question.

The course is free of charge. Contact us ( for enquiries.

Nordic Microscopy Symposium – 3rd-5th October

We are delighted to invite you to the Nordic microscopy symposium at the Live Cell Imaging core facility, Nikon Centre of Excellence at Karolinska Institutet, organised by BergmanLabora, Ramcon Denmark and Inter Instrument AS.

  • The symposium will highlight the great research done in the Nordics where microscopy is a key tool.
  • New exciting equipment from Nikon will be showcased including the AX/NSPARC super-resolution point confocal and the CrEST DeepSIM super-resolution spinning disk confocal.
  • We will also be launching the new Nikon Eclipse Ji benchtop assay instrument and demo the simpler CrEST Cicero spinning disk confocal.
  • The capability of these systems will be demonstrated during public sessions (3rd of October) and in private sessions (on 4th and 5th October) where you are welcome to bring your own samples.

Venue: Neo, Flemingsberg Campus, Karolinska Institute: Erna Möller Lecture hall (Symposium), Live Cell Imaging (LCI) core facility (Demos)

3rd October

    • 1000-1145       Public demo: Nikon AX R NSPARC super-resolution point-scanning confocal, CrEST X-Light V3 super-resolution spinning disk confocal, CrEST Cicero compact spinning disk
    • 1000-1145       Open house at the Live Cell Imaging core facility (Drop in. Contact Sylvie Le Guyader)
    • 1200-1300       Lunch (requires pre-registration)
    • 1300-1305       Welcome
    • 1305-1345       Zuzana Kadlecova (Cambridge Institute for Medical Research – UK): Lights! Camera! Uptake! Zooming in on Endocytosis with Quantitative TIRF-SIM Analysis.
    • 1345-1410       Nicoline Dorothea Daugaard (Dept. Biochemistry and Molecular Biology, SDU – Denmark): Tracking T cells and their interactions with cancer cells in 3D using NIS-Elements General Analysis (GA3)
    • 1410-1440       LCI short talks:
      • Chiara Annunziata (Karolinska Institute – Sweden): A pipeline for the multiparametric assessment of the anti ageing effects of candidate molecules
      • Andrea Coschiera (Karolinska Institute – Sweden): Primary cilia promote the differentiation of human neurons through the WNT signaling pathway
      • Natalie Geyer (Karolinska Institute – Sweden): Multiplex RNA in situ hybridisation for liver parenchyma characterization in a metastatic context
    • 1440-1500       Coffee
    • 1500-1525       Technical talk (Nikon): Microscopy Simplified, Nordic Launch of Nikon’s new ECLIPSE Ji
    • 1525-1540       Staffan Strömblad (Karolinska Institute – Sweden): Multi-site assessment of reproducibility in high-content cell migration imaging data
    • 1540-1605       Pieta Mattila (University of Turku – Finland): Advanced imaging methods to visualize lymphocyte activation

4th and 5th October

Registration is mandatory and can be done via the following site: Nordic Microscopy Symposium – BergmanLabora.

Please share this event with friends and colleagues who may also be interested in attending.

Clearing and expansion microscopy symposium and workshop sept 12-14

Two really nice symposia/workshop on clearing and expansion microscopy next week!

The power of Deep Neural networks

I am wowed at the images published recently in BioArxiv in the Zero-shot deconvolution networks paper. It will be interesting to see the peer-reviewed paper.

I would be interested in visualizing the amount of errors made by the network. A simple way to do it is to acquire a short time lapse (eg 10 images) of a fixed sample, run it through the network and see which structures are stably identified and which change from frame to frame. 🙂


Light-seq: Multiplexed, non-destructive spatial transcriptomics of tissues sections using light

Light-Seq is a new pretty cool technique for highly multiplexed sequencing of RNA in tissue sections using light. This technique is highly sensitive, highly spatially resolved and because it does not destroy the tissue, it can be combined with protein labelling (genetic or by immunolabelling).

On one of our single-point confocal/spinning disk/widefield system at the LCI facility, we have a device called Primo (DMD + UV laser) which can be used to run this technique! 🙂

Let us know if you would like to set up LightSeq at the LCI core facility!

Live demo of the Nikon Mizar TILT light sheet

On the 22nd of September at 10, you get a chance to see and try the latest light sheet on the market: the Nikon Mizar TILT.

    • Easy to use stage top light sheet with only 1 objective
    • Imaging of cell monolayer, cells in gels, organoids in gels, small organisms…
    • Samples in glass bottom multiwell chamber slides
    • Stage top incubator for live sample imaging
    • Advantage of using the TILT light sheet
      • low phototoxicity and bleaching even with high resolution objective
      • excellent temporal and spatial resolution for live samples
    • See here for more info.

This demo is only for a limited time (10 days) and in person only. Please let us know if you want to join the demo and if you want to try your own sample.

Live demo of the Crest spinning disk with DeepSIM

9th of September, 10-12am: Live/zoom demo of the latest microscope acquired by the LCI facility: Crest spinning disk with DeepSIM (new Orion)

  • Ti2 microscope
  • Crest spinning disk (identical to the one on Tweety but with slightly different wavelengths)
  • DeepSIM: SIM is a fast super-resolution technique which is gentle for the sample (less bleaching, less photodamage for live samples) and offers double the resolution of a confocal microscope (down to 120nm resolution), even thick in samples. It is flexible and can be used with any objectives, even low magnification air objectives.
  • No specific sample preparation requirements
  • More information here

For the best experience, join the demo in person at the LCI facility (please apply by replying to this email) but if you cannot make it, you can also listen on Zoom.

The system has been purchased by the LCI so it is here to stay! 🙂

Please let us know if you want to join the demo in person and mention if you would like to try imaging your own sample with DeepSIM.

mCherry-XL: brigther, more stable and with better spectra!

mCherry is a very popular red fluorescent protein. However it has several disadvantages:

  • It is shifted towards far red (ex peak 585 nm) so it often is not imaged optimally with the illumination sources and filters commonly available.
  • It bleaches fast

mCherry has now been evolved into mCherry-XL with several improvements:

  • This variant is shifted back towards green (ex peak 560 nm) therefore being very well excited with popular 561nm lasers.
  • It is 3 times brighter than mCherry
  • There is also a clear improvement in the lifetime for FLIM
  • Together the 2 points above means that less excitation power is required so it should help with the bleaching problem

Here is the paper. Therefore you should consider mCherry-XL for your future tagging with red fluorescence proteins.

Super resolution STED event at Scilife in March

Nordic superresolution microscopy facility staff/researchers: STED

March 15th and 16th at 9-12 am. CONTACT: Hans Blom (

Mar 15, 2022 9:00am

  • 9:00-9:45am – BNMI info / STED intro [Hans Blom & Daniel Smeets (Leica)]
  • 9:45-10:15am – STED sample prepping [Ulf Schwarz et al. (Leica)]
  • Break
  • 10:30-11:00am – Input from a Nordic STED facility [Jonathan R. Brewer (DaMBIC)]
  • 11:00-11:45am – STED demos [Luis Alvarez/Ulf Schwarz et al. (Leica)]
  • 11:45-12:00amExtra discussion time

Mar 16, 2022 9:00am

  • 9:00-9:45am – Live-cell STED [Giovanna Coceano (KTH Stockholm)]
  • 9:45-10:15am – Remote STED [Marko Lampe (ALMF/EMBL)]
  • Break
  • 10:30-11:00am – STED-FCS [Erdinc Sezgin (KI Stockholm)]
  • 11:00-11:45am – Advanced STED demos [Luis Alvarez/Ulf Schwarz et al. (Leica)]
  • 11:45-12:00amExtra discussion time

Follow us! :-)

Type your email address below to subscribe to our blog!