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.
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.
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
Welcome to the first meeting of the Bridging Nordic Microscopy Infrastructures (BNMI) network that will take place at the University of Iceland in Reykjavík, Iceland August 17-19 2022. Registration and more info: https://bnmi.hi.is