Tutorials
Learn SciPathJ step by step with our comprehensive guides
Getting Started with SciPathJ
This comprehensive tutorial covers everything you need to get started with SciPathJ, from installation to your first successful segmentation.
- Complete installation walkthrough
- Interface and navigation overview
- Step-by-step first segmentation
- Tips for optimal results
All Tutorials
Browse our complete collection of tutorials
Getting Started with SciPathJ
Learn the basics of SciPathJ, including installation, interface overview, and your first segmentation.
Image Segmentation Deep Dive
Comprehensive guide to segmenting cells, nuclei, cytoplasm, and vessels from H&E images.
Training Custom Classifiers
Learn how to define custom cell classes and train XGBoost models for automated classification.
Batch Processing Workflows
Process entire folders of images efficiently with batch processing techniques.
Feature Extraction & Analysis
Understand the 150+ features extracted and how to use them for downstream analysis.
Integration with ImageJ/Fiji
Use SciPathJ as a plugin within ImageJ or Fiji for seamless workflow integration.
Recommended Learning Path
Follow this sequence for the best learning experience
Start with Basics
Complete the "Getting Started" tutorial to understand the interface and basic workflow.
Master Segmentation
Learn detailed segmentation techniques for different tissue components.
Explore Features
Understand the extracted features and how to use them for analysis.
Train Classifiers
Create custom cell classes and train machine learning models.
Automate Workflows
Set up batch processing for efficient analysis of large datasets.
Additional Resources
Supplementary materials to support your learning