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Microscopy data analysis: machine learning and the BioImage Archive

  • Overview
  • Search
  • Course content
  • Introduction to bioimage analysis
    • Introduction to image analysis
    • Deep learning introduction
    • Segmentation with StarDist and SplineDist
  • Bioimaging data resources at EMBL-EBI
    • BioImaging data resources at EMBL-EBI – an overview of the BioImage Archive, BioStudies and EMPIAR
    • BioImaging data resources at EMBL-EBI – practical
  • Open access machine learning resources for bioimage analysis
    • ZeroCost – Practical
    • BioImage Model Zoo – lecture
    • BioImage Model Zoo – practical (DL4MicEverywhere)
    • Ilastik – practical
    • Cellpose – practical
    • CellProfiler
      • CellProfiler – lecture
      • CellProfiler – practical
  • Image Data Resource – Discovery using community repositories
    • Image data resource – introduction
    • Image data resource – Data submission and curation
    • Image data resource – Practical
  • Advanced computational topics in the context of bioimage analysis
    • pyTorch introduction
    • Advanced topics (Terminal, Snakemake, pyTorch)
    • Distributed/Cloud computing
  • Technical help sheet
  • Trainer biographies
  • Further learning
    • The Electron Microscopy Public Image Archive – EMPIAR
      • Introduction to EMPIAR
      • MitoNet and EBI/EMPIAR
      • Using vEM data with napari and EMPANADA – practical
    • Terminal, Snakemake, pyTorch – Practical
    • deepImageJ
    • ImJoy
  • Your feedback

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Open access machine learning resources for bioimage analysis

This section introduces the following community-led AI resources for bioimage analysis:

  • ZeroCostDL4Mic – practical
  • BioImage Model Zoo – lecture
  • BioImage Model Zoo – practical
  • Ilastik – practical
  • Cellpose – practical
  • CellProfiler
    • Lecture
    • Practical

  • page navigation-left-circle-1_1 BioImaging data resources at EMBL-EBI – practical
  • pageZeroCost – Practical navigation-right-circle-1_1