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.
Nordic superresolution microscopy facility staff/researchers: STED
March 15th and 16th at 9-12 am. CONTACT: Hans Blom (email@example.com)
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)]
- 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
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)]
- 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
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
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
- 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
- AI, Super Resolution microscopy
- 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! 😃
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
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!
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.
You can join the Switzerland’s Image and Data Analysis School, ZIDAS 2021.
This one-week school provides a hands-on introduction to image processing and analysis, with an emphasis on biologically relevant examples.
This school is for you if…
* you are a life-science researcher with a pressing need to quantify your light-microscopy images.
* you are uncertain about how to: Best calculate co-localisation, do deconvolution, automate the counting of cells, track objects over time, handle massive amounts of image data, record your image-analysis workflows in a reproducible manner.
More information can be found here: https://2021.zidas.org/
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 29th 14:00 – Dr Carlo Beretta from Heidelberg University on “How to build a Bioimage Analysis Workflow with multiple image analysis tools”
- July 6th 14:00 – Dr Marko Popovic from Nikon Centre of Excellence in Amsterdam on “Quantitative pathology”
Program and free registration: here.
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.
This MOOC for undergrad students by the University of Montpellier is about labeling and imaging vertebrate embryos.
All the videos are also available on their YouTube channel.
As far as I know, this is the first pure microscopy MOOC (Massive Open Online Course), dealing with sample preparation, imaging and data handling!
If you know of another microscopy MOOC (I know of some image analysis MOOC but not microscopy), please leave me a comment or sent me an email! 🙂