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 broadcast of all public lectures the LCI microscopy course

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

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

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

30 Jan – 17 Feb 2023

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

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

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!

BII webinar about a great tool! TissUUmaps

The BioImage Informatics facility at Scilife organizes a new presentation on free and open-source tools: TissUUmaps, a browser-based tool for GPU-accelerated visualization and interactive exploration of millions of datapoints overlaying tissue samples.

Users can visualize markers and regions, explore spatial statistics and quantitative analyses of tissue morphology, and assess the quality of decoding in situ transcriptomics data. TissUUmaps provides instant multi-resolution image viewing, can be customized, shared, and also integrated in Jupyter Notebooks. TissUUmaps was created in collaboration between BIIF and the Wählby lab. You can read more about it and test the software on its web page: https://tissuumaps.github.io/
During the seminar, we will go through basic usage of TissUUmaps: installation, loading images, markers and regions, change visualization settings, and how to load / save / share projects. The webinar will be given by Christophe Avenel and will take place on March 3rd, 09:00-10:00 (instead of our normal Call4Help session). There will be time for questions and discussion, so we hope this event to be very interactive. Please register here.

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! 😃

BII webinars and Global Bioimaging lectures

Lots of interesting courses and webinars about microscopy in these corona times. The BioImage Informatics facility at Scilife will present how useful it is to build imaging pipelines with Fiji/imageJ.

April 6th, 10:00-11:00: “ImageJ/Fiji – Make Your Own Macros – Overview”. This is not to teach how to script but to give you an overview of the scripting possibilities in ImageJ/Fiji. Please register here.

Version 2.0 of TissUUmaps is now released: TissUUmaps allows fast interactive display of tissue slide images and uses an overlay to display any sort of marker data on top. Be it spatially resolved gene expression, per cell data, or regions of interest. TissUUmaps is developed in the Wählby-Lab, with involvement of BIIF, and was first published in https://doi.org/10.1093/bioinformatics/btaa541.
Try out TissUUmaps and interact with a in-situ-sequencing dataset on a brain slice!

Advanced Methods in Bioimage Analysis, Online EMBO Practical Course, 26 Jun – 2 Jul 2021; Registration Deadline: 5 Apr 2021
This advanced course concentrates on teaching cutting-edge concepts and tools for quantitative image analysis, and will seek to upgrade the competencies of future bioimage analysis experts on both theoretical algorithm advancements as well as on practical implementation skills. BIIF is part of the scientific organization team. Register here.

Global BioImaging-ZEISS webinar series in Light Microscopy

Check here to see some nice general microscopy webinars by Global Bioimaging, the global pendant to Euro Bioimaging:

  • Tuesday, 30th March at 15:00 CEST: Introduction to Confocal Microscopy.
  • Tuesday, 20th April at 15:00 CEST: Multi-colour imaging – where are the limits & what are the opportunities?
  • Tuesday, 11th May at 15:00 CEST: Super-resolution: What is it? How can you do it? What does it enable?
  • TBA: From 2D to 4D imaging – how switching to a sheet of light has revolutionised volume acquisitions in Life Science.
  • TBA: Methods for Clearing your specimens – what are the options and which should you choose?
  • TBA: Automation in modern microscopy: easy ways to prevent costly accidents and enable your users with tools for easy experimental set up.

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!

Gisele got the Chan Zuckerberg Initiative grant!!

Congratulations to our dear in-house image analyst Gisele Miranda who got the prestigious Chan Zuckerberg Initiative grant in December! 🙂

Gisele got this grant thanks to the fruitful collaboration between the BioImage Informatics facility at Scilife and the Live Cell Imaging facility at KI. We are delighted for her and for all the LCI users as this will allow us to keep working with Gisele for many years.

Congratulations Gisele! Very well-deserved! 🙂

Look at what CZI has chosen as their symbol of Science: a microscope!

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