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Dear All,

this newsletter we would like to point you to our upcoming webinar on TissUUmaps 3.1. Also, there are many courses with BIIF involvement approaching, spanning different topics like basic theory of microscopy, image analysis concepts, Deep Learning, and more.

Call4Help webinar on TissUUmaps 3.1

We are organizing a new webinar on TissUUmaps, a 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.
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.
Date: February 14, 10:00-12:00 on Zoom.
More information and registration here.


LCI microscopy course – From sample preparation to image analysis.

The LCI microscopy course provides the theoretical and practical knowledge to properly use hard- and software in a microscopy based experiment. Including image analysis.

More Information: LCI course
Dates: January 30 – February 17, 2023 - Lectures are broadcasted live on Zoom!

NBIS workshop in Neural Nets and Deep Learning

This course 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

More information and registration here.
Application deadline: February 10, 2023

Digital image analysis for scientific applications

This course aims at giving doctoral students and researchers from different disciplines sufficient understanding to solve basic computerized image analysis problems. The course will also offer an introduction to a number of freely available software tools, preparing the participants to start using computerized image analysis in their own research. The course will be in a hybrid format.
More information available here.
Application deadline: February 25, 2023

Writing ImageJ Macros - Uppsala universitet

This course is suitable for those familiar with ImageJ and want to learn automating the analysis. You will be able to efficiently use the same protocol on multiple images, get much greater control over the image analysis, and provide a full description of the analysis for the methods section of publications. No experience of writing software needed. The course is organized by Jeremy Adler, Biovis, Uppsala.
Where and when: Rudbecklab, Uppsala, March 20th 9.30-4.30.
More information and contact:

Best regards
Anna, in behalf of BIIF

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