Presentation

COMPUTER OPTIMIZED MICROSCOPY

                     A practical image analysis course for life sciences



AIM OF THE COURSE:


The Computer Optimized Microscopy Course is directed to  researchers (microscopy facility stuff members, pre and post-docs, PIs, etc.) who work with digital images  obtained by a range of optical microscopy techniques. The course provides a series of mixed theoretical and practical sessions aimed to show the image processing workflow needed to extract quantitative information over different basic and advanced microscopy techniques. From beginning to end, a first general view of image processing basics will be followed by a more detailed focusing on specific applications.


WORKING TOOLS: 


The open source ImageJ / Fiji software will be used as a main tool for the course.  For some specific applications, other open source and commercial softwares may be also utilized, thus providing a wider range of solutions to specific image processing problems.



GENERAL SUBJECTS:


Parameters to optimize image acquisition

Introductions to some useful Fiji tools

Image restoration: filters

Image restoration: deconvolution

Segmentation and binnary operations

Automation of the process: Introduction to the macro language



SPECIFIC APPLICATIONS:

         

Colocalization of molecules

          Cell tracking

          3D reconstruction

          ratio FRET and FRAP analysis

Macro programming of some specific applications already seen

          High content screening

          Machine learning