Tag: Workshop

Spatial transcriptomics in Flemingsberg!

Spatial transcriptomics techniques are booming! It is now possible to identify where RNAs are located within a tissue! At the LCI facility, we routinely image samples labelled with RNAscope. If you use RNAscope, you might be interested in this workshop where you will learn how to label thick samples with RNAscope, and this symposium about automated RNAscope.

Additionally, we can now offer the 10x Genomics Visium technology on the South Campus, as a collaboration between 4 core facilities in Flemingsberg: LCI, FENO, SICOF and BEA core facilities!

Here is the workflow:

  1. We discuss your project and advise you for the preparation of your sample.
  2. You cut your sample and optimize the antibody or H/E staining yourself, under the guidance if the LCI staff to best preserve the RNAs.
  3. You image your tissue sections at the LCI facility.
  4. You transfer your section to SICOF who tags the RNAs and amplifies the library, using the 10x Genomics Visium technology.
  5. The library goes to BEA for sequencing.
  • Section size: max 6.5×6.5 mm or max 11×11 mm
  • Human or mouse
  • Paraffin-embedded or fresh-frozen
  • Labelled with H/E or fluorescent antibodies

Come and talk to us about your Spatial Transcriptomics project!

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!

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.

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 (hblom@kth.se)

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)]
  • 11:45-12:00am – Extra discussion time

https://kth-se.zoom.us/j/69376340781

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)]
  • 11:45-12:00am – Extra discussion time

https://kth-se.zoom.us/j/67902191893

Listen to the lectures at the LCI facility microscopy course!

Starting from next week, the Live Cell Imaging core facility at KI will run its yearly microscopy course.

All the course lectures and some workshops will broadcasted live on Zoom, free of charge and there is no need to register.

Name: Microscopy: improve your imaging skills – from sample preparation to image analysis

Date: 24 Jan – 11 Feb 2022

Target audience:

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.

The course covers the following topics:

  • Optics, image formation
  • Fluorescence, fluorophores
  • Bleedthrough
  • Anatomy of a microscope
  • Objectives and refraction index
  • Cameras and detectors
  • Noise and background, Bit depth and saturation
  • Multichannel imaging and spectral unmixing
  • Resolution and contrast
  • Sample preparation, Immunostaining
  • Nyquist sampling
  • Confocal and wide field settings
  • Speed, High throughput/content
  • Volume imaging, deconvolution
  • Clearing and expansion
  • Live cell imaging
  • Fourier
  • AI, Super Resolution microscopy
  • Colocalization
  • Data handling, OMERO.figure

On this page, you can find the course schedule (public activities are in blue) and the  Zoom link to join. Scroll down to read the student testimonies! 😊

Hope you enjoy the Live Cell Imaging core facility microscopy course 2022! 😃

The LCI microscopy course 2022 is now open for registrations!

It is now time to apply to the intensive LCI microscopy course Jan/Feb 2022: Microscopy: improve your imaging skills – from sample preparation to image analysis

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 their knowledge is limited.

All the lectures at the LCI microscopy course will also broadcasted live online, free of charge and there is no need to register.

All details about the course including course schedule, how to apply, and how to follow the lectures are found here.

Scroll down to read the kind testimonies of our dear students! 😊

Hope you enjoy the LCI facility microscopy course 2022!

The first microscopy MOOC?

This MOOC for undergrad students by the University of Montpellier is about labeling and imaging vertebrate embryos.

All the videos are also available on their YouTube channel.

As far as I know, this is the first pure microscopy MOOC (Massive Open Online Course), dealing with sample preparation, imaging and data handling!

If you know of another microscopy MOOC (I know of some image analysis MOOC but not microscopy), please leave me a comment or sent me an email! 🙂

The LCI microscopy course 2021 starts next week! :)

As usual the lectures at the LCI microscopy course will broadcasted live online, free of charge and there is no need to register.

Title: Microscopy: improve your imaging skills – from sample preparation to image analysis

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.

Applications are closed but all lectures will be broadcasted live and open to anyone without registration.

The course covers the following topics:

  • Optics, image formation, fluorescence, fluorophores, microscope and microscopy types
  • Objectives and refraction index, Cameras and detectors
  • Noise and background, Cameras and detectors, Bit depth and saturation, Multicolour imaging
  • Resolution and contrast, Sample preparation, Immunostaining
  • Nyquist sampling, Confocal and wide field settings, Scaling up and speeding up, High throughput/content
  • Volume imaging, deconvolution, multiphoton, Clearing and expansion
  • Live cell imaging, Fourier, AI, Super Resolution microscopy
  • Data handling, OMERO.figure, Requirements for image analysis, Colocalization
  • Image processing and analysis

Check the course schedule and details of how to join the Zoom webinars. Scroll down to read the kind testimonies of our dear students! 😊

Here is the course syllabus.

Hope you enjoy the LCI facility microscopy course 2021!

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