Cool technique – Page 2 – The Live Cell Imaging facility

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.

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. 🙂

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!

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

9^th 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.

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.

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

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!