Bioimaging is a central set of tools in Biological research. It is interdisciplinary science which requires understanding of biology, microscopy, fluorescence probes, image processing and image analysis. Tremendous volumes of multi-dimensional biological data are now being generated in almost every branch of biology. How to visualize and how to interpret such images in quantitative, objective and efficient way is essential knowledge for students who use bioimaging for their research.
The course will cover useful techniques and tools used for analysis of images in Biology. Topics that will be addressed include: basic concepts of digital images, visualization of multi-dimensional data, image processing in preparation for analysis, noise and image enhancement, binary operations, object / particle analysis and intensity and morphometric measurements, tracking for analysis of particles or cells movement, filament analysis, colocalization and deconvolution.
We will address the issues of image ethics and proper image acquisition for image analysis. We will introduce the students with two image analysis software: the free ImageJ/Fiji package and the commercial Imaris software. We will focus on examples and hands-on exercises that will teach a broad functionality of these tools and the concepts needed for building suitable workflow for a given application.
A whole module is dedicated to workflow building and analysis automation using scripting with ImageJ macro language. We do not assume previous programming background.
The course include a Bring-Your-Own-Data module, in which students present their own image analysis applications, and everyone discuss possible approaches for solutions. Finally the students apply the learned tools to their own data, with help of the course teachers, to get a head start with image analysis for their own research.