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Course Outline
Introduction to Fiji and ImageJ
- An overview of Fiji and its diverse applications in scientific research
- Understanding the architecture of ImageJ and its plugin ecosystem
- Installation and configuration of Fiji for optimal performance
Basic Image Processing Techniques
- Image acquisition and supported import formats
- Adjusting contrast, brightness, and applying various filters
- Methods for image stacking and projection
Advanced Image Analysis
- Segmentation techniques, including thresholding and edge detection
- Object counting and particle analysis within histological samples
- Measuring areas, perimeters, and other morphological features
Working with Biological Samples
- Processing images of histological tissues, blood cells, and algae
- Colour deconvolution and the analysis of stained tissues
- Time-lapse analysis and tracking cell movement
Automation and Customization
- Developing and executing macros for repetitive tasks
- Leveraging Fiji plugins for specialised analyses
- Introduction to scripting using the ImageJ Macro Language (IJM)
Data Management and Reporting
- Exporting results and generating comprehensive reports
- Annotating images and preparing data for publication
- Best practices for ensuring reproducible image analysis
Requirements
- A foundational understanding of biological imaging concepts
- Exposure to microscopy and histological techniques
- Essential computer literacy skills
Target Audience
- Researchers specialising in biotechnology and environmental toxicology
- Laboratory technicians engaged in histological and cellular imaging
- Scientists interested in applying quantitative image analysis methods
14 Hours
