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Fully open source and powerful software suite

How the brain works is not understood and it remains a major challenge for biologists. Wouldn't it be nice to have a map of it, so that at least we know where is what? This map would have to show all the necessary detail — the synapses between neurons, and the finest and smalles dendrites — and such data can only be obtained using high-resolution imaging with electron microscopy. However even the smallest brains, such as the brain of a tiny fruitfly, are gigantic structures on the scales offered by electron microscopes.  

A recent paper in PLoS Biology describes computer assisted analysis of the entire Drosophila larval brain that combines electron and light microscopy data to integrate the brain’s micro and macro architecture. It is a culmination of a long-term collaboration between researchers from the Institute of Neuroinformatics ETH Zurich (Albert Cardona), the Department of Molecular Cell and Developmental Biology UCLA (Volker Hartenstein) and the MPI-CBG (particularly Stephan Saalfeld).

The Dresden team contributed the registration algorithm for large serial section TEM and the Collaborative Annotation Toolkit for Massive Amounts of Image Data (CATMAID) designed for Google maps-style navigation and basic annotation of the massive electron microscopy datasets. The analysis of the data is in its infancy and new, better datasets are in the works, however the major contribution of this fruitful collaboration, spearheaded by Albert Cardona, is the development of fully open source and powerful software suite TrakEM2 for acquisition, registration, navigation, and segmentation of light and EM neuroanatomy data. TrakEM2 is distributed through Fiji and is actively used by the leading electron microscopy labs around the world. All papers, software and data are Open Access showing the way of how science should be done in the 21st century.

Movies Capture:
Visualization of globally optimal registration of  a small ssTEM tile system consisting of a single 6x6 layer (Movie 1) and 3 layers 4x4 tiles each (Movie 2). The approach scales to very large tile systems made of tens of thousands of individual images.

References:
Albert Cardona, Stephan Saalfeld, Stephan Preibisch, Benjamin Schmid, Anchi Cheng, Jim Pulokas, Pavel Tomancak, Volker Hartenstein (2010):
An Integrated Micro- and Macroarchitectural Analysis of the Drosophila Brain by Computer-Assisted Serial Section Electron Microscopy.
PLoS Biol 8(10): e1000502. doi:10.1371/journal.pbio.1000502

Stephan Saalfeld, Albert Cardona, Volker Hartenstein, and Pavel Tomancak:
As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets
Bioinformatics (2010) 26(12): i57-i63 doi:10.1093/bioinformatics/btq219

Stephan Saalfeld, Albert Cardona, Volker Hartenstein, and Pavel Tomancak:
CATMAID: collaborative annotation toolkit for massive amounts of image data
Bioinformatics (2009) 25(15): 1984-1986 doi:10.1093/bioinformatics/btp266