Author: NMI

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NMI node receives funding from the Chan Zuckerberg Initiative

The Centre for Cellular Imaging (CCI) at the University of Gothenburg has been awarded funding from the Chan Zuckerberg Initiative through their imaging program to Advance Imaging Through Collaborative Projects. CCI will take part in two different projects where prof. Julia Fernández-Rodríguez will be co-PI:

COMULISglobe: Multimodal Imaging across Scales in Life Sciences, to harness the power of multimodal imaging across scales from basic research to clinical diagnostics, facilitate access, and train a new generation of scientists

Society for Knowledge Exchange in BioImage Analysis (NEUBIAS), to secure the sustainability of the Network of European Bioimage Analysts, establish strong connections to similar initiatives, and share knowledge about state-of-the-art bioimage analysis tools and methods

You can find more information at the Chan Zuckerberg Initiative website

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TissUUmaps 3: Interactive visualization and quality assessment of large-scale spatial omics

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

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EMBL course on Advanced fluorescence imaging techniques

Do you want to learn how to derive qualitative and quantitative insights on molecular mechanisms in cells and developing organisms? Then join ‘Advanced fluorescence in imaging techniques’, a hands-on course for researchers using light microscopy equipment to solve biological problems at the cellular and molecular level in vivo.

Organizer: EMBL Heidelberg
Location: EMBL Advanced Training Centre
Time of event: May 7-12, 2023
Deadline for registration: February 12, 2023
Weblink: https://www.embl.org/about/info/course-and-conference-office/events/mic23-02/?utm_source=EMBL+courses+and+conferences&utm_campaign=ad0cc26a4e-MIC23-02+announcement&utm_medium=email&utm_term=0_-ad0cc26a4e-%5BLIST_EMAIL_ID%5D#vf-tabs__section-53de8397-0f08-449c-b4a4-0fdca47249f2
Contact: lea.hohmann@embl.de

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Basic Course in Scanning and Transmission Electron Microscopy (SEM/TEM) for Physical Sciences

This course covers lectures and practical demonstrations in SEM and TEM techniques. The contents include principles of focused electron and ion beam microscopy, specimen preparation for EM imaging and advancements in electron microscopy such as high-resolution TEM, scanning TEM, electron diffraction, elemental analysis and in-situ electron microscopy.

NMI node: UCEM at Umeå University
Location: Lectures at KBC Building and laboratory demonstrations at UCEM, Umeå
Time of event: February 21-23, 2023
Deadline for registration: February 14, 2023
Weblink: https://www.umu.se/en/research/infrastructure/medicinska-fakulteten/u/umea-centre-for-electron-microscopy-ucem/courses-workshops-and-training/basic-course-feb-2023/
Contact: linda.sandblad@umu.se

You can find more info on UCEM’s courses here: https://www.umu.se/en/research/infrastructure/medicinska-fakulteten/u/umea-centre-for-electron-microscopy-ucem/courses-workshops-and-training/

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BioImage Informatics CALL4HELP

The BioImage Informatics Facility (BIIF) together with microscopy expert Sylvie Le Guyader (LCI, Karolinska Institutet) organizes a Call4Help session every month. The aim is to offer combined expertise towards microscopy and bioimage analysis. All researchers from Swedish institutes can participate.

NMI node: BIIF at Uppsala University
Location: on zoom
Time of event: every 1st week of the month (mainly on Tuesdays, but there might be exceptions)
Deadline for registration: continuous
Weblink: https://www.scilifelab.se/call4help-form/
Contact email: biif@it.uu.se

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NBIS workshop in Neural Nets and Deep Learning

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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PhD course on Digital Image Analysis for Scientific Applications (DIASA)

The target group is PhD students from all subjects where digital image analysis (IA) is used as a research tool. No previous experience in IA is required from the course participants, but an interest in its potential as a tool in their own research is important. The course can be followed with a basic knowledge of mathematics (corresponding to upper‐ secondary level entry requirements) and basic computer skills.

NMI node: BIIF at Uppsala University
Location: Dept. IT, Uppsala University and on zoom
Time of event: second half of spring 2023
Deadline for registration: February 10, 2023
Weblink: https://www.teknat.uu.se/education/doctoral-studies/courses/faculty/2023-image-analysis-for-scientific-applications-digital/
Contact: carolina.wahlby@it.uu.se

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