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Presentation Information     2011-01-31 (15:15)   •  The seminar room at Vi2

Speaker Johan Henriksson
Comment Department of Biosciences and Nutrition, Karolinska Institutet
Type External presentation
Title Endrov - an open source framework for image processing and analysis
Abstract During our work on Virtual-Worm Base (a database of spatio-temporal gene expression patterns during C. elegans development), we found that the current tool chain for microscopy is insufficient. Commercial software could not be modified for our purposes since we lack the source code. The expense and format lock-in makes it hard to spread to other labs. ImageJ, the defacto-standard image software, is not designed for modern needs and has become only a patchwork trying to add the missing features.

To solve these problems we have developed a new platform - Endrov (www.endrov.net) - that covers the entire microscopy chain. It is a plug-in framework consisting of 140 000 lines of Java, running on all operating systems. The following are Endrov's features:
- It has advanced control of the microscope hardware (via Micro-manager)
- It can view, annotate, process and analyze recordings. New applications are introduced with the graphical programming language (flows), interpreted Java or new plugins. Endrov can also be used as a library, making heavy data analysis simple.
- There are at the moment about 130 image processing filters and 80 plugins
- A new schema for data storage which handles arbitrary metadata, 6D recordings, mixed resolutions and compression (both lossy and lossless).
- Large datasets are handled gracefully. Moreover, the speed of most operations is unaffected by the size of datasets.
- Endrov supports most file formats (via Bio-formats)
- Image servers like OMERO are supported (still in experimental stage)

Our framework is open and free of charge. It is highly flexible and can be adopted to any needs in current research. As an application, we have used our framework to quantify a large number of genes' expression levels.