BIIF Newsletter, December 2021

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Dear All,

we want to highlight the upcoming NEUBIAS Academy webinar featuring Wei Ouyang (KTH) with ImJoy. Also below again the information about two upcoming courses.

NEUBIAS webinar - Introduction to ImJoy: AI-powered image analysis on the web

Presenter: Wei Ouyang (KTH)
7 December, 2021, 15h30-17h00
Registration here.
More information on the NEUBIAS Academy website.

ImJoy (https://imjoy.io) is a web-based computational platform for building interactive data analysis tools. ImJoy is ideally suited for building interactive image visualization, annotation and anlysis tools, especially for handling with large datasets and running AI models on remote servers.

ImJoy is also used to power ImageJ.JS (https://ij.imjoy.io) which serves ~800 users per day. With our recent development, the ImJoy AI Server provides an efficient way for multi-model serving and enables hassle-free training and inference.

Basic introduction to deep learning, web image analysis and ImJoy – Session 1:

Develop your own ImJoy plugin We will demonstrate how to build an ImJoy plugin in ImJoy for image visualization, annotation and processing using other ImJoy plugins such as ITK/VTK viewer, Vizarr, Kaibu and ImageJ.JS. The participants can follow step-by-step and build their own ImJoy plugins.

Session 2: Train your own deep learning model with the ImJoy AI Server

In this session, we will introduce our recent development in the ImJoy AI Server for model training and inference. You will learn how to interact with the server to run popular deep learning models and also train your own U-Net or CellPose model.

Courses

There are two courses coming up in which we are involved.

Digital image analysis for scientific applications – focus MAX IV

The course aims at giving doctoral students and researchers from different disciplines a sufficient understanding of digital image processing and analysis techniques to solve basic image analysis problems. The content of the course includes methods especially suitable for MAX IV data. The course will also offer an introduction to several freely available software tools (e.g. CellProfiler, ImageJ, and ilastik), preparing the participants to start using computerized image analysis in their research.

More information: https://www.cb.uu.se/~damian/DIASA_2022/

Application deadline: December 15

NBIS workshop in Neural Nets and Deep Learning

This course will give an introduction to the concept of Neural Networks (NN) and Deep Learning. Topics covered will 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: https://www.scilifelab.se/event/nbis-workshop-in-neural-nets-and-deep-learning/

Application Deadline: December 05

Call4Help

The next Call4Help session is coming up on December 7, information here.
Note that you can always contact us under biif@scilifelab.se to set-up a meeting and receive support on image analysis.
The idea of the Call4Help session is to provide combined support on both the image analysis and the microscopy part of a project.

Best regards Anna
on behalf of BIIF

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