Cool technique – Page 2 – The Live Cell Imaging facility

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!

Jennifer Lippincott-Schwartz excellent talk on November 8th

Scilifelab invited Jennifer Lippincott-Schwartz to give a talk IRL in Solna on November 8th. Jennifer works a lot with microscopy and is an excellent speaker so her talk is guaranteed to be inspiring!

Here is more info.

What can Artificial Intelligence do for you?

Check out the Nikon Artificial Intelligence (NIS.ai) webinar series to understand how Ai can help you in your microscopy experiments.

The NIS.ai Webinar Series will take place on Tuesdays at 14:00hrs and we are delighted to announce the first two talks:

June 29^th 14:00 – Dr Carlo Beretta from Heidelberg University on “How to build a Bioimage Analysis Workflow with multiple image analysis tools”
July 6^th14:00 – Dr Marko Popovic from Nikon Centre of Excellence in Amsterdam on “Quantitative pathology”

Program and free registration: here.

Artificial Intelligence tools

Artificial Intelligence, Deep Learning and Neuronal Networks are taking over the world, including microscopy. Within the next couple of years, you might well end up wondering how you got anything done without them!

Having an idea how Artificial Intelligence, Deep Learning and Neuronal networks work means that you will be able to come up with ideas about how they can help you in your research.

The Neubias (Network of European image bioanalysts) webinars and meetings are a good place to learn.

Here are 2 upcoming webinars about tools to train and use AI algorithms.

From Images to Knowledge virtual workshop

Nov 30th-Dec 2nd, Janelia Research Center organizes a great image analysis workshop with loads of goodies. Everything is online and free. There are in depth and more general workshops about Deep Learning with different freeware, programming and scripting of all sorts, Big data things… Check the program here.

Super resolution course and webinars at ALM

Dear all

See here for more details about the ALM super resolution microscopy course in January. Note that the webinars are open to everyone (see registration email at the bottom of the page) and are always very interesting talks. 😊