Thursday, 3 March and Friday, 4 March, 2011
Barcelona Science Park (PCB)

Dates

Thursday, 3 March, 2011 (9.00-17.00) and Friday, 4 March, 2011 (9.00-17.00)
+ optional ‘users data session on Friday, 4 March, 17.00-20.00)

Venue

Sala 1, Torre D, Barcelona Science Park (PCB), Baldiri Reixac, 10

Speakers/Teachers

• Kota Miura, Centre for Molecular and Cellular Imaging, EMBL (Heidelberg, Germany)
• Timo Zimmermann Advanced Light Microscopy Unit, CRG (Barcelona, Spain)
• Sebastien Tosi, Anna Lladó, Julien Colombelli Advanced Digital Microscopy, IRB Barcelona (Spain)

Aim and Context

Image J has become an essential tool in many fields of Life & Material Sciences dealing with scientific Images. It is free, easy-to-use, and integrates a huge and complete choice of tools to process, analyze, measure, quantify, visualize or edit scientific data from Images. Backed-up by a community of scientists and programmers who constantly work on developing ImageJ to integrate the latest tools within Plugins and Macros, Image J constantly improves, develops and evolves. The key-feature of Image J is its extensibility.

This course will focus on one of these scripting tools, the Macro Language, and aims at teaching to advanced ImageJ users the main tricks to perform automated Image processing with ImageJ. The course will last 2-days, and will alternate theoretical parts on image processing and programming theory with practical hands-on sessions. Our long term goal is to build up a local community of Image J users (in Spain) who can share knowledge and tools and we believe the macro language is one of these tools, which should help a large number of scientists.

Course content

• Macro Basics: Syntax, Variables, Strings, Operators.
• How to Call ImageJ Functions: the Macro Recorder.
• Automating a Macro: Conditions, Statements and Loops, User Decision vs. Computer Decision
• Saving and Manipulating Results: Data Input/Ouput, Dialog Boxes, File Input/Output
• User Defined Functions: Exercises on Stack Manipulation, Time Series, Particle Analysis.
• Debugging Macros, Batch Processing Mode.
• Advanced Macro Programming examples applied to specific Image Processing topics: segmentation, filtering, 3D counting, tracking, etc.

Participants

The course is addressed to scientists and microscopy specialists working in Spain in the Life Sciences and who work regularly with Image J and would like/need to use it more thoroughly in their research/facility. A large part of the course will be hands-on with laptop computers (not provided), and will require a strong commitment from the participants to actively learn how to program. This course is not an introduction to ImageJ and is not adapted for people who do not use Image J on a regular basis. For more information, please contact: microscopyirbbarcelona.org.

Participation is free of charge and is limited to 30. Lunches and coffee breaks are included. Participants are expected to organize and cover their travel and accommodation expenses.

Participants need to bring their own laptop (PC or Mac) to perform the hands-on sessions (60% of the course). We strongly invite selected participants to present a poster to share ideas on their research and their needs/development in Image Processing.