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Course Outline
Introduction to Fiji and ImageJ
- Overview of Fiji and its applications in scientific research for government and academic institutions
- Understanding the architecture of ImageJ and its plugin ecosystem
- Installing and configuring Fiji for optimal performance in a laboratory or office setting
Basic Image Processing Techniques
- Image acquisition methods and supported import formats
- Adjusting contrast, brightness, and applying various filters to enhance image quality
- Image stacking and projection techniques for comprehensive analysis
Advanced Image Analysis
- Segmentation techniques including thresholding and edge detection for precise object identification
- Object counting and particle analysis in histological samples for detailed biological assessments
- Measuring areas, perimeters, and other morphological features to support quantitative research
Working with Biological Samples
- Processing images of histological tissues, blood cells, and algae for accurate biological studies
- Color deconvolution and analysis of stained tissues to enhance visualization and interpretation
- Time-lapse analysis and tracking cell movement to understand dynamic processes
Automation and Customization
- Creating and executing macros for automating repetitive tasks in image processing workflows
- Utilizing Fiji plugins to perform specialized analyses tailored to specific research needs
- Basic scripting with the ImageJ Macro Language (IJM) to customize analysis routines
Data Management and Reporting
- Exporting results and generating comprehensive reports for documentation and sharing
- Annotating images and preparing data for publication in scientific journals and government reports
- Best practices for ensuring reproducibility in image analysis processes for government and academic research
Summary and Next Steps
Requirements
- A foundational understanding of biological imaging concepts for government research and applications
- Familiarity with microscopy and histological techniques used in governmental laboratories
- Basic computer literacy to navigate digital tools and software for government use
Audience
- Researchers in biotechnology and environmental toxicology working for government agencies
- Laboratory technicians engaged in histological and cellular imaging for government projects
- Scientists interested in quantitative image analysis within the context of government research
14 Hours
