LCI event – 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.

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 Live Cell Imaging facility is Nikon Center of Excellence – Symposium and open house – tomorrow 10/11

Tomorrow, we will celebrate us being Nikon Center of Excellence with great microscopy talks, a live demo of the latest Nikon Ax confocal and guided tours of the LCI facility!

Join us IRL if you have registered or follow the talks on Zoom with this link (scientific program below).

You can also join us physically from 13:50 onwards for the Ax demo or the guided tour. Remember to book a time slot on the paper in front of the Erna Möller seminar hall in Neo.

9:00 – 9:05 Welcome (Staffan Strömblad)
9:05 – 9:15 Sylvie Le Guyader
Presentation of the Live Cell Imaging Core Facility
9:15 – 9:45 Christophe Leterrier, CNRS-Aix Marseille University, France
Looking at neurons at the nanoscale with super-resolution microscopy
9:45 – 09:50 Dusan Popov, European Product Manager Super Resolution, Nikon Europe B.V.
Future of superresolution imaging
9:50 – 10:05 Jianjiang Hu, Karolinska Institutet
Local temporal Rac1-GTP nadirs and peaks restrict cell protrusions and retractions
10:50 – 11:20 Joakim Lundeberg, The Royal Technology Institute, Stockholm, Sweden
Exploration of the transcriptome and genome in a tissue context
11:20 – 11:50 Guillaume Jacquemet, Åbo Akademi, Finland
Democratizing deep learning microscopy image analysis (ZeroCostDL4Mic)
11:50 – 11:55 Simone Lepper, European Product Manager Imaging Software & High- Content Screening, Nikon Europe B.V.
Future of Image Analysis
13:00 – 13:50 Featured presentation: Jennifer Lippincott-Schwartz, Senior Group Leader, Howard Hughes Medical Institute, Janelia Research Campus, USA
Emerging Imaging Technologies to Study Cell Architecture, Dynamics, and Function
13:50 –16:00 Open house at the Live Cell Imaging Core Facility / Tours / Demos

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 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

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!

LCI microscopy course, vintage 2021 :)

The Live Cell imaging facility will run again its intensive light microscopy course in Jan-Feb 2021.

The schedule can be found here.

As usual, all lectures will be publicly broadcasted live. So if you think that a lecture could be useful for you, you are welcome to listen, without registration, by following this link.

Due to the current pandemics, only registered students will be allowed in the lecture room.

The course comprises lectures, workshops, imaging of your own sample, demos… It will run 26 Jan-12 Feb, 3 days/week (tues-thurs) 9:00-17:15.

There are only 16 spots. The course counts for 6 credit points.
The rest of the time (the course counts for 4 weeks) is used for home assignments. Mondays and Fridays will also be used for individual workshops where we image your own sample.

The application process is open now until the 16^th of November. Please read carefully the eligibility criteria. You will need to sent me some images of your sample at the time of application. This course is only open to people who already have some experience of fluorescence microscopy.

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

At the end of the course, the participants will be able to:
1- Describe the difference between wide field, confocal and light sheet microscopes as well as the different types of confocal microscopes and choose which system is most suited to their experiments
2- Pick the best combination of fluorophores for their experiment by matching their spectra with the microscope light source and filters, identify and eliminate bleed-through and cross-excitation problems
3- Explain objective specifications and limitations and choose the appropriate objective for their own experiments
4- Describe how to fix, mount and handle their sample in a way that is optimal for imaging
5- Find their sample and the area of interest without bleaching it
6- Adjust the condenser for proper DIC imaging (Koehlering)
7- Explain how to set the following parameters on a wide field, a confocal or a light sheet system to best match the requirements of their sample and reliably answer their scientific question: resolution, pixel size, averaging, scan speed, illumination power, detector gain and offset, camera readout rate, exposure time and camera binning
8- Explain which applications require a hardware or a software autofocus, a spectral detector, a resonance scanner, two-photon or super resolution microscopy
9- Explain the advantages in using the automation of a microscope system to collect multidimensional data
10- Explain how to deal with images before publication in scientific journals
11- Describe the imaging requirements for automated image analysis
12- Run an image analysis pipeline on freeware (ImageJ/FIJI, Cell Profiler) designed for their own images and scientific question.

Please spread the word to your colleagues.

We are looking forward to meeting you and your sample! 😃

Tweety turned into a power machine!

Our dear Tweety microscope, which was simplest and cutest of all the LCI systems, has muted into our most sophisticated power machine!

On the 24^th at 10, we will run an online demo (link below) to show what our upgraded Tweety can deliver:

Much larger field of view (from 18 mm diagonal to 25 mm)
Upgraded single point confocal on the left side
Resonant scanner with 1024×1024 pixels (compared to 512×512 on our other resonant scanners), still the same speed (30 fps) and improved low noise
Spinning disk confocal on the right side with bypass to image wide field
2 very sensitive cameras on the right side: one with the very large field of view and 11um pixels for best sensitivity and one with the normal field of view and 6.45 pixels for best resolution
Our great Primo is still on the back of the microscope to allow micropatterning of proteins at the bottom of a dish or micromanufacturing of wells in the shape/pattern of your choice
2 wonderful silicon immersion objectives specialized for tissue imaging with automatic correction ring: 20x/1.05 and 40x/1.25

After the demo, the LCI users who have already been trained on our widefield systems can get access to Tweety for free after a mandatory short training.

Please add the demo in your calendar and make sure to test the link ahead of the meeting.

Link to the Zoom Meeting on the 24^th at 10am: https://ki-se.zoom.us/j/7302561100

Broadcasted lectures from the LCI microscopy course and private demos of light sheet and cameras

Our course starts tomorrow! 😀

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 and want to improve their skills.

Registrations are closed but all lectures are open to everyone without registration.

The schedule and details of the venue are here.
All lectures are also available online live. The link and instructions to watch are here.
Make sure you check the schedule in case of last minutes changes.

If you are in Sweden, you are welcome to try some of the equipment on demo with your own sample.

To book at timeslot, please contact the responsible person directly.

Light sheet microscope from M2Lasers: Valentina Loschiavo Valentina.Loschiavo(at)m2lasers.com
- Fast imaging of large sample
- Overview function to navigate in the sample and find the region of interest
- 800x800um field of view with 1um min resolution
- Any immersion media
- Sample size up to centimetres
Wide Field microscope from Nikon with 3 different Andor cameras: Oliver Garner (oliver.garner(at)bergmanlabora.se)
- Nikon Ti2 microscope with 4 times larger field of view
- A front illuminated sCMOS camera: Good sensitivity and resolution, great speed, but a greyish background (Andor Zyla 4.2)
- A back-illuminated EM-CCD camera: highly sensitive camera with very dark background, but lower resolution and lower speed (Andor 897U)
- A back-illuminated sCMOS camera: same sensitivity and low background as an EM-CCD but better resolution and speed (Andor Sona)

Seminar on how to directly label your primary antibodies: Skip the secondary, part 3!

The LCI will host a seminar about GlyCLICK, a new way to directly label primary antibodies and stop using secondaries: 6th of November at 13:00 in the Lipid seminar room in Neo, KI Flemingsberg. The seminar will be broadcasted live. Here is how to find us and here how to follow the seminar online.

Everyone agrees that it would be great to be able to label our samples without using secondary antibodies.

less animals killed
shorter and cheaper protocols
no problem with isotype cross-reaction
no problem with secondary species when using many antibodies at once

There are many kits to label primary antibodies directly with fluorophores. The main disadvantage compared to primary/secondary stainings is that direct labels are often weaker because the final primary/fluorophore ratio is too low. Using an amplification method like TSA (Tyramide Signal Amplification) leads to a loss of resolution.

Over the years users at the LCI have tried this kit, this kit and this one. They gave mixed results depending on the antibody but we keep looking! Come to the LCI seminar about a new direct labelling technique that uses Click chemistry.