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Course Outline
Introduction to Fiji and ImageJ
- Overview of Fiji and its applications in scientific research
- Understanding ImageJ’s architecture and plugins
- Installing and setting up Fiji for optimal performance
Basic Image Processing Techniques
- Image acquisition and import formats
- Adjusting contrast, brightness, and applying filters
- Image stacking and projection methods
Advanced Image Analysis
- Segmentation techniques: thresholding and edge detection
- Object counting and particle analysis in histological samples
- Measuring areas, perimeters, and other morphological features
Working with Biological Samples
- Processing images of histological tissues, blood cells, and algae
- Color deconvolution and analysis of stained tissues
- Time-lapse analysis and tracking cell movement
Automation and Customization
- Creating and running macros for repetitive tasks
- Using Fiji plugins for specialized analyses
- Basic scripting with ImageJ Macro Language (IJM)
Data Management and Reporting
- Exporting results and generating reports
- Annotating images and preparing data for publication
- Best practices for reproducible image analysis
Summary and Next Steps
Requirements
- Basic understanding of biological imaging concepts
- Familiarity with microscopy and histological techniques
- Basic computer literacy
Audience
- Researchers in biotechnology and environmental toxicology
- Laboratory technicians working with histological and cellular imaging
- Scientists interested in quantitative image analysis
14 Hours
