The LCI open microscopy course starts on Monday! :)

Dear all

It is my pleasure to invite you to follow the LCI facility microscopy course Microscopy: improve your imaging skills – from sample preparation to image analysis.

The course starts next Monday (29 Jan) and runs until the 16th of February.

As usual, all the course lectures are broadcasted live on Zoom. It is free of charge and you do not need to register.

The aim for this course is to improve the microscopy skills of students and researchers who have already used a microscope to acquire digital images of fluorescent samples but feel that more knowledge could help them.

Here is a selection of what we will talk about:

  • Optics and image formation,
  • Anatomy of a microscope
  • Objectives and refraction index
  • Cameras and detectors, Noise and background, Bit depth and saturation
  • Sample preparation, Immunostaining, Clearing and expansion
  • Resolution and contrast, Nyquist sampling, Microscope settings
  • Data handling, OMERO.figure, Requirements for image analysis, Colocalization
  • Image processing and analysis

Check our course webpage to see the course schedule (Broadcasted activities are in blue) and the Zoom link. Scroll down to read the kind testimonies of our dear students! 🙂

Here is the course syllabus.

For those who are on a far away time zome, we record all the live lectures and post them every evening on the LCI facility YouTube channel! 🙂

We hope that you will enjoy the LCI facility microscopy course!

Kindly forward to anyone who might be interested.

The LCI team

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 (LiveCellImaging@ki.se) for enquiries.

Time to register to the LCI microscopy course!

Dear all

It is time to enroll to the yearly light microscopy course run by the Live Cell imaging core facility (29 Jan – 17 Feb 2024): Microscopy: improve your imaging skills – from sample preparation to image analysis’ (6 credits).

  • Check the course schedule 2024 and the syllabus to see the course content and alumni testimonies.
  • Postdocs or registered PhD students can apply to the course.
  • Please read carefully the eligibility criteria in the syllabus and note that the last registration date is the 15th of November.
  • 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 on the course page.

The purpose of this course is to enable PhD students and researchers who have already and recently used a microscope to acquire images of fluorescent samples, to improve their microscopy skills.

The course is NOT aimed at training people to use the LCI facility microscopes. The focus is instead on providing the students with enough theoretical and practical knowledge about their OWN sample and their OWN microscope, to enable them to:

1) prepare their sample and formulate their scientific question in a way that is suitable for data extraction from fluorescence images

2) properly use the hardware available in their lab/facility and 3) fully understand each parameter they need to set in the software in their lab/facility.

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

Please help us spread the word. 😃

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!

Nordic microscopy symposium – Save the date!

Please join the Nordic microscopy symposium on the 3rd of October at the Live Cell Imaging core facility, Nikon Centre of Excellence at Karolinska Institutet. The symposium is organised by BergmanLabora, Ramcon Denmark and Inter Instrument AS. Please save the date.

The event will highlight Nordic research where light microscopy is a key tool.

Several Nikon fast super resolution systems will also be available: Nikon AX confocal with NSPARC and Nikon/CrEST V3 spinning disk with DeepSIM.

Before and after the symposium, the capability of these systems will be demonstrated during public sessions (on the 3rd of October) and in private sessions (booking required) where you are welcome to bring your own samples.

Preliminary schedule:

Tuesday 3rd October

1000-1045     AX R NSPARC + CrEST V3 with DeepSIM public demonstration (in parallel)

1100-1145        AX R NSPARC + CrEST V3 with DeepSIM public demonstration (in parallel)

1200-1300     Lunch (requires pre-registration)

1300-1305     Welcome

1305-1345      *Keynote: TBC

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 Institutet – Sweden)

Andrea Coschiera (Karolinska Institutet – Sweden)

Natalie Geyer (Karolinska Institutet – Sweden)

1440-1500     Coffee

1500-1525      *Super resolution system overview (Nikon): Title TBC

1525-1540      *Staffan Strömblad (Karolinska Institutet – Sweden): Multi-site assessment of reproducibility in high-content cell migration imaging data

1540-1615       *Pieta Mattila (University of Turku – Finland): Title TBC

Wednesday 4th October

0830-1400    AX R NSPARC + CrEST V3 with DeepSIM private demonstrations (bring your own sample)

Thursday 5th October

0830-1400    AX R NSPARC + CrEST V3 with DeepSIM private demonstrations (bring your own sample)

Venue (symposium): Erna Möller Lecture hall, Neo, Flemingsberg Campus, Karolinska Institutet

Venue (system demonstrations): Live Cell Imaging core facility, Neo, Flemingsberg Campus, Karolinska Institutet

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

Cool stuff one can do with the LCI Primo

At the LCI core facility, you can use a machine called Primo to micropattern/print proteins at the bottom of a microscopy dish and enable real time imaging of cell-protein interactions.

Now we learnt that we can even micropattern lipids and antibodies on microscopy dishes to image how cells interact with these molecules! This can be done with any pattern and even in multiwell plates! 🙂

Lipid micropatterning: Here is a cool paper showing how filopodia interact with sourrounding lipids and proteins. They image with Structured Illumination and TIRF, techniques that are also on offer at our facility. 🙂

Antibody micropatterning: A new way to analyse extracellular vesicles with multiplexed detection of proteins and RNAs at single EV resolution.

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.

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