Introduction to Image Analysis with Fiji

About

In this two-day workshop, we will introduce basic concepts of image analysis and intermediate workflows using Fiji. By the end of this workshop, you will be able to automate the bulk of your image analysis, making it faster, more consistent and reproducible.

Automated microscopy technologies have amplified the volume and complexity of image data such that biologists must rely on computer scientists for solutions and software. Fiji provides a huge variety of advanced image analysis solutions and a friendly user interface for researchers to develop innovative, cutting-edge pipelines for biological image analysis. Users range from non-programmers to bioinformaticians and software engineers to professional computer science researchers. Biologists without programming skills can use Fiji to search for biologically relevant features (segmentation), to follow relevant objects across space and time (tracking) and to compare specimens through mapping to anatomical or cellular digital atlases. Those skilled in programming can use scripting languages in Fiji to build custom image-processing pipelines. Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji is Just ImageJ.

Participants do not need to have any previous knowledge of the tools that will be presented at the workshop, but must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) Please download and install Fiji before the workshop.

Syllabus 

Image Processing with Fiji

• Digital Image Formation
• Introduction to ImageJ and Fiji
• Stacks and Hyperstacks
• Measurements
• Segmentation
• Tracking
• Stitching
• Colocalization Analysis
• Batch Processing
• Scripting