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Microscopy image analysis materials 2021

  • Overview
  • Search
  • Course content
  • Introduction to image analysis
    • Introduction to image analysis
    • ZeroCostDL4Mic: Exploring Deep-Learning in microscopy
    • Segmentation with StarDist and SplineDist
    • Practical session on machine learning
  • Introduction to bioimage databases and resources
    • The BioStudies database
    • The BioImage Archive
    • EMPIAR
    • IDR – Image Data Resource
  • Image analysis tools
    • Bioimage Model Zoo
    • Cell profiler
  • Trainer biographies
  • Technical help sheet
  • Further learning
  • Your feedback

Creative Commons

All materials are free cultural works licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, except where further licensing details are provided.

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Practical session on machine learning

Trainer: Craig Russell, Romain Laine & Maria Theiss

Overview:  In this session you will learn about managing and preparing your data for machine learning.

Learning outcomes

By the end of this session you will be able to:

  • Describe workflow management systems and their benefits
  • Build and run a Snakemake pipeline

Materials:

  • Presentation slides
  • Images
  • Snakemake demo
  • StarDist folder
  • Docker – Containerisation for scientific computing
  • page navigation-left-circle-1_1 Segmentation with StarDist and SplineDist
  • pageIntroduction to bioimage databases and resources navigation-right-circle-1_1