Fiji: Image Processing for Biotechnology and Toxicology Training Course

Introduction to Fiji and ImageJ

• Overview of Fiji and its applications in scientific research for government agencies
• Understanding the architecture of ImageJ and its plugin ecosystem
• Installing and configuring Fiji to ensure optimal performance in a public sector environment

Basic Image Processing Techniques

• Methods for image acquisition and supported import formats
• Adjusting contrast, brightness, and applying various filters to enhance image quality
• Techniques for image stacking and projection to facilitate comprehensive analysis

Advanced Image Analysis

• Segmentation techniques including thresholding and edge detection
• Object counting and particle analysis in histological samples for government research
• Measuring areas, perimeters, and other morphological features to support detailed studies

Working with Biological Samples

• Processing images of histological tissues, blood cells, and algae for government laboratories
• Techniques for color deconvolution and analysis of stained tissues in a public sector setting
• Time-lapse analysis and tracking cell movement to support dynamic biological studies

Automation and Customization

• Creating and executing macros for repetitive tasks to enhance efficiency in government workflows
• Utilizing Fiji plugins to perform specialized analyses tailored to public sector needs
• Introduction to basic scripting with the ImageJ Macro Language (IJM) for enhanced customization

Data Management and Reporting

• Exporting results and generating comprehensive reports for government use
• Annotating images and preparing data for publication in scientific journals
• Best practices for ensuring reproducibility in image analysis for government research

Summary and Next Steps