BIIF Newsletter, February 2022

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This month’s newsletter is full of learning opportunities. We are organizing a new tool webinar presenting TissUUmaps; have recorded a QuPath tutorial video and participated with a lecture on bioimage analysis to the LCI microscopy course. See more information below.

Call4Help Tool webinar

We are organizing a new presentation on free and open-source tools. This time we will present TissUUmaps, a browser-based tool for GPU-accelerated visualization and interactive exploration 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. 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 go through basic usage of TissUUmaps: installation, loading images, markers and regions, change visualization settings, and how to load / save / share projects. The webinar will be given by Christophe Avenel and will take place on March 3rd, 09:00-10:00 (instead of our normal Call4Help session). There will be time for questions and discussion, so we hope this event to be very interactive. Please register here.

Learning resources

New video: QuPath introduction

We have uploaded a new video to our YouTube channel. This is an introduction to QuPath – a free and open software for digital pathology - with focus on multiplexed fluorescence microscopy data. It starts from creating a project, covers cell detection + classification, and ends with the detection of blood vessels and spatial analysis. Video link

LCI course - Microscopy: improve your imaging skills - from sample preparation to image analysis

Last month the Live Cell Imaging (LCI)core facility, KI, gave its intensive microscopy course. Recordings of the lectures are available on YouTube. Here you can also find Gisele’s lecture – an introduction on bioimage analysis.

Conferences

I2K 2022 – From Images to Knowledge (virtual event)

The 2022 virtual event “From Images to Knowledge (I2K)”, to be held from May 6th, 9th and 10th, will feature talks and in-depth interactive workshops covering state-of-the-art open-source solutions for biological image reconstruction and analysis, as well as social interaction between developers, researchers, and students. It will be an event to learn about and discuss forward looking strategies for dealing with the ever-increasing amount of large and content rich microscopy imagery.
More information: https://coba-nih.github.io/i2kconference/

BNMI symposium – Bridging the Nordic Microscopy Infrastructure

The Bridging Nordic Microscopy Infrastructures network (BNMI) is a collaboration between Nordic imaging infrastructures that aims to enhance interactions between the different infrastructures and countries, increase visibility of the available infrastructures and create interactive networks in life science imaging. The first meeting of the BNMI network will take place at the University of Iceland in Reykjavík, Iceland August 17-19  2022.
More information: https://bnmi.hi.is/

Best regards
Anna, in behalf of BIIF