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🤖 Getting Started with AI

  • Introduction to Google Colab
  • The PyImageJ AI Notebook
  • Prompt Engineering

🚀 Getting Started (Traditional)

  • Installation
  • How to initialize PyImageJ

🪄 How-to guides

  • Tutorial notebooks
  • Using PyImageJ without a screen
  • Troubleshooting

🔬 Use cases

  • imagej-ops
  • Integration
  • Segmentation
    • Blob detection (interactive)
    • Blob detection (headless)
    • Classic Segmentation
    • Cellpose/StarDist Segmentation
    • Puncta Segmentation
  • Other use cases

🛠️ Development

  • Developing PyImageJ

📚 Reference

  • API
  • Citation
PyImageJ
  • Segmentation use cases
  • Edit on GitHub

Segmentation use cases

These are use cases demonstrating segmentation workflows with PyImageJ

  • Blob detection (interactive)
  • Blob detection (headless)
  • Classic Segmentation
    • Segmentation workflow with original ImageJ functions
    • Segmentation workflow with ImageJ2
  • Cellpose/StarDist Segmentation
  • Puncta Segmentation
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