This one-week school provides a hands-on introduction to image processing and analysis, with an emphasis on biologically relevant examples.
Covered topics will encompass :
- Basics in Image Formation
- ImageJ, from everyday use to advanced applications
- State-of-the-art analysis procedures like e.g. co-localisation
- Machine Learning including Deep Learning
- Stitching and registration
- Data analysis using KNIME
This training session will cover the basics of super resolution in photonic microscopy, principally: STED microscopy (STimulated Emission Depletion) and single molecule localization microscopy. We will also present alternative solutions for super resolution like SRRF (Super resolution Radial Fluctuations), Airy Scan, or Computer based pixel-reassignment like ISM (Image Scanning Microscopy), and solution based on light sheet illumination. The mornings will be dedicated to theoretical lectures and application seminars. The afternoons will allow the participants to see demonstrations of these different techniques in front of home-made or commercial systems. The fourth day will be a full hands-on day, as participants will be invited to bring their own samples and test them on the different systems available, like STED microscope, STORM, lattice light sheet, ISM, SRRF….
Rapid advances in live imaging of targeted cellular morphologies and functions underpin the emerging revolution in our understanding of synapses, circuits, and behaviour. In keeping with its long-established tradition, this Cajal course will assemble at its international faculty leading experts in developing and exploiting cutting-edge imaging techniques that have been propelling such advances. How to combine genetically encoded fluorescence labelling with behavioural designs, micro-circuit monitoring, or single-molecule tracking, how to avoid pitfalls of having false-positive observations and inherent noise, how to best analyse your multi-dimensional data will be, among others, the recurrent subjects of the Course.
The use of fluorescence microscopy (wide field, confocal, multiphoton, and now superresolution) in combination with genetically encoded fluorescence probes comprise a powerful set of scientific tools to study live cells. However, surprising little practical and theoretical training in such methods exists within standard curricula, particular at the early stage of training (Masters or Doctorate level). This course offers to cover basic optics principles necessary to understand the origin of microscope resolution and design. Participants will get hands-on experience implementing simple optical configurations to illustrate these fundamental principles. Subsequently, participants will perform experiments on state-of-the-art imaging equipment provided by microscope vendors.
This training school will cover the basics of image analysis using ImageJ/Fiji, as well as image analysis workflow automation using ImageJ macro programming. In addition, it will be taught how to use the software package ilastik for machine learning based image segmentation and object classification, and how to integrate ilastik into ImageJ macro based workflows. Moreover, an overview of further relevant bioimage analysis software packages will be given and there will be ample time for "Work on Your Own Data" sessions assisted by experienced Analysts.
This school targets bioimage analysts, who are willing to enhance their professional scope and techniques for improving the quality of their analysis, as well as willing to contribute with their knowledge and experience to the school. Prerequisite is a proficiency in at least one programming language (we do not train coding). The school focuses on workflow designing. This year, we will have a particular emphasis on statistics for bioimage analysis and related tools e.g. R and Python libraries. In addition, we will overview machine & deep learning components.
Microscopie à épi-fluorescence et microscopie confocale: Des bases à la pratique