Workshops – NMI

Course: 4th CryoNET Advanced Image Processing Workshop, June 2026

Title: 4th CryoNET Advanced Image Processing Workshop
Time of event: 22-26 June 2026
Location: KBC building, Umeå University, Umeå, Sweden
Deadline for registration: 1 June 2026
Weblink: https://www.umu.se/en/cryonet-workshop-2026/

The aim of the course is to provide training in cryoEM image processing including the latest developments in the field to intermediate or advanced users.

The course is open for facility users or potential facility users, such as PhD students, postdocs, and researchers within the life sciences who are curious and will profit from cryoEM skills. Swedish and international course participants are welcome. To attend, the course participants should be familiar with electron microscopy and structural biology.

Participants will receive an overview and hands-on training in state-of-the-art techniques for single particle cryoEM image processing, model building, validation, and tomographic workflows from a range of guest lecturers by international specialists. The course also includes plenty of opportunity for discussions during the week, which should facilitate the participants to tackle their own research challenges.

Participation in the entire course is mandatory, and an attendance certificate will be given at the end of the course.

This course is supported by SciLifeLab, CryoNET and Umeå University and organized by the Umeå Centre for Electron Microscopy (UCEM).

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

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