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

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

CCI Seminar: Introduction to MALDI-Imaging Mass Spectrometry

We are happy to announce that CCI now can offer MALDI-Imaging Mass Spectrometry technology. We would like to give our gratitude to Jörg Hanrieder and his group for allowing us to open and offer this fantastic instrument and technology to our users!

And to celebrate this collaboration on the 28th of April from 13:00 to 15:00 we have organised an Online seminar: Introduction to MALDI-Imaging Mass Spectrometry

13:30-14:00
Mass Spectrometry Imaging – A new dimension of chemical microscopy
Jörg Hanrieder, Associate Professor (Docnet) Department of Psychiatry and Neurochemistry, University of Gothenburg, Sweden
14:00-15:00
Elemental and molecular imaging – integrating spectroscopic techniques into MS workflows

Martina Marchetti-Deschmann, Professor at the Institute of Chemical Technologies and Analytics, Vienna University of Technology, Austria

Register to receive a link for the seminar: https://docs.google.com/forms/d/e/1FAIpQLSdKuMT4DteoprJXQfSZohMMMIaiCi4mkOFuKTrBhyq-tG5LXg/viewform

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