Cool service – Page 2 – The Live Cell Imaging facility

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

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!

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.

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

Where to find microscopy jobs, forums and wikis

Where to ask microscopy-related questions?

– Image.sc and microlist
Post your microscopy, sample preparation and image analysis questions

– Confocal server
Old email-based forum that is followed by tons of people across the globe as well as most microscopy companies. Post your microscopy and sample preparation questions.

Freeware for image analysis

– Image J/Fiji
Great freeware to open images acquired on any microscope, resize, crop, change contrast, create movies, annotate, analyze and much more.

– Cell Profiler
Freeware for automated image analysis including machine learning.

– KNIME
Open source to build a custom made image analysis pipeline

– Icy
Great freeware to open images acquired on any microscope, resize, crop, change contrast, create movies, annotate, analyze and much more.

Networks, jobs and career

The European Light Microscopy Initiative (ELMI)

Light microscopy jobs, meetings, courses, networking… in Europe. Remember to mail them that you want to show up on their map of European microscopy!

Euraxess

Loads of information from which companies/institute works with research to how to find an apartment when moving to another lab, find work, know your rights, express your opinion about researchers’ work conditions…

Science Career development plan

Other places to look for work:

Microscopy wikis

– Kurt Thorn’s excellent microscopy blog
I highly recommend this blog even if it is not updated anymore. Monthly digest of major microscopy related articles. Loads of tips.

– Microscopy Education by Nikon

– Leica Science Lab

– Microscopy Education by Olympus

– Microscopy Education by ZEISS

– Molecular Expressions

– SVI deconvolution

– Microscopy info

– Nature Milestones Light Microscopy

– iBiology Microscopy Course