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ImJoy

ImJoy – practical session

Trainer: Wei Ouyang

This session was a part of the 2022 iteration of this course.

Overview:  ImJoy (https://imjoy.io) is a web-based computational platform for building interactive data analysis tools. It is developed to address the challenges in deploying AI-powered image analysis tools. By utilizing the recent advances in the web and Python ecosystem, ImJoy is ideally suited for building and sharing interactive image visualization, annotation and analysis tools, especially for handling large datasets and running AI models on remote servers. ImJoy is also used to power ImageJ.JS (https://ij.imjoy.io) which is a web version of the classic ImageJ image analysis software and it serves ~800 users per day. With our recent development on a computational backend for serving AI models, named BioEngine, it makes building interactive AI-powered image analysis tools even easier.

Note: Interactive slides and notebooks will be provided during the practical session, please note that you will need the latest Google Chrome browser to get the best compatibility for developing ImJoy plugins.

Learning objectives:

After this session you should be able to:: 

  • Identify basic concepts in web-based image analysis and ImJoy
  • Develop your own ImJoy plugins for image visualization and annotation
  • Use BioEngine to do deep learning based image analysis
  • Interact with the BioEngine server to run popular deep learning models such as CellPose for image segmentation

Materials:

Presentation and materials

This practical assume basic Python and web programming skills, if you are not familiar with them, please read the recommendations parts here: https://imjoy.io/docs/#/i2k_tutorial. Feel free to also go through the interactive tutorial if you want to understand more about ImJoy plugin development.

Recent massive natural language processing models allow generating Python code from English instructions, this has a great potential to revolutionize bioimage analysis. To learn more, watch this “sneak peek into the future” video: https://www.youtube.com/watch?v=pkOp_oUybsc

Recording: