Fiji: Image Processing for Biotechnology and Toxicology

• 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

Fiji is an open-source image processing package based on ImageJ, tailored for scientific image analysis, especially in biological research.

This instructor-led, live training (online or onsite) is aimed at beginner-level to intermediate-level researchers and laboratory professionals who wish to process and analyze images related to histological tissues, blood cells, algae, and other biological samples.

By the end of this training, participants will be able to:

• Navigate the Fiji interface and utilize ImageJ’s core functions.
• Preprocess and enhance scientific images for better analysis.
• Analyze images quantitatively, including cell counting and area measurement.
• Automate repetitive tasks using macros and plugins.
• Customize workflows for specific image analysis needs in biological research.

Format of the Course

• Interactive lecture and discussion.
• Lots of exercises and practice.
• Hands-on implementation in a live-lab environment.

Course Customization Options

• To request a customized training for this course, please contact us to arrange.

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