National Microscopy Infrastructure
The advanced light microscopy (ALM) node of NMI welcomes you to a SciLifeLab workshop together with Zeiss on dynamical microscopy. It will cover imaging modalities such as AIRY, lattice lightsheet and FCS/DP, including quality control and image analysis. There will be a combination of technical information and applications, as well as parallel demo sessions.
Time of event: March 6, 2024
Location: SciLifeLab, Tomtebodavägen 23, Solna, Sweden
Registration: hans.blom@scilifelab.se
The Centre for Cellular Imaging, which is the national SciLifeLab facility for Correlative Array Tomography in Sweden, has the great pleasure to welcome you to the first Cellular 3D volume – Correlative Array Tomography (CAT) Workshop! It is designed to bring experts, researchers and industry together interested in Cellular 3D volume – CAT to introduce this new technology, stimulate knowledge exchange and the formation of collaborations.
Organizer: The NMI node Centre for Cellular Imaging
Location: Wallenberg Centre & Centre for Cellular Imaging, Gothenburg, Sweden
Time of event: Nov 29 – Dec 1, 2023
Registration: https://forms.office.com/e/5jzrEWDmCH
Weblink: https://www.gu.se/en/core-facilities/centre-for-cellular-imaging/cat-workshop-2023
Contact email: cci@gu.se
We present TissUUmaps, browser-based tool for GPU-accelerated visualization and interactive exploration of tens 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. It is also possible to directly connect spatial markers with markers in feature space, such as UMAP plots, to interactively relate feature space with physical space. 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 specifically showcase new features of TissUUmaps 3.1, such as:
– HDF5 / AnnData files loading
– Network diagram visualization
– Multiple datasets displayed on a grid
– Plugin engine
The webinar will be given by Christophe Avenel and Fredrik Nysjö.
Organizer/NMI node: BIIF at Uppsala University
Location: Online
Time of event: 10:00-12:00, February 14th, 2023
Deadline for registration: February 14, 2023
Weblink: https://www.scilifelab.se/event/tissuumaps-3-interactive-visualization-and-quality-assessment-of-large-scale-spatial-omics-2/
Contact: christophe.avenel@it.uu.se
This course is provided by the National BioInformatics Infrastructure Sweden (NBIS) and gives an introduction to the concept of Neural Networks (NN) and Deep Learning. Topics covered include:
• NN building blocks, including concepts such as neurons, activation functions, loss functions, gradient descent and back-propagation
• Convolutional Neural Networks
• Recursive Neural Networks
• Autoencoders
• Best practices when designing NNs
Location: Navet, SciLifeLab, Uppsala
Time of event: March 20, 2023 – March 24, 2023
Deadline for registration: February 10, 2023
Weblink: https://www.scilifelab.se/event/nbis-workshop-in-neural-nets-and-deep-learning-2/
Contact: edu.neural-nets-deep-learning@nbis.se
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