ESPINA software tool allows to study brain structure in greater depth

Nov 10 2011

Researchers at the UPM and CSIC, within the Cajal Blue Brain project, develop ESPINA, a new freeware software tool that allows to study the brain structure in greater depth.

Its use will allow to explore new hypotheses in order to improve the understanding of the human brain or to seek new solutions in the fight against diseases such as Alzheimer's, epilepsy and Parkinson's.

Resulting from a research in the context of the Cajal Blue Brain project, researches at the (CeSViMa, Facultad de Informática, CTB) and CSIC (Laboratorio Cajal de Circuitos Corticales) have developed ESPINA, a freeware software tool that allows to extract new information about the brain structure. In particular, from three-dimensional images obtained by an electron microscope, the expert can semi-automatically analyze the different structures present on digital images of the brain tissue, such as synapses, mitochondria, vesicles, axons, dendrites and so on.

The research has focused on counting synapses in different layers of the cerebral cortex. The analysis of the results will establish new hypotheses about the organization of neuronal connections. The study is being applied to different species, including humans. Some of the results1,2 have been published in various scientific journals and have been reported in several international conferences.

The main features of ESPINA cover 3D exploration of the tissue scanned, segmentation of the relevant structures to neuroscientists, 3D reconstruction of previously segmented brain structures, or extraction of new parameters to characterize every segmented structure as well as sets of these structures.

ESPINA is implemented using the programming language Python and is designed using free distribution tools, such as Qt for GUI development, VTK for displaying three-dimensional data or ITK for processing the images, which has also allowed to distribute it freely. ESPINA is a multiplatform tool, being in operation on computers with Linux or Windows.

At present there is no similar software tool taking into account the singular nature of the data that is able to process as well as the functionality implemented. Thanks to ESPINA experts have accelerated the analysis of the data available with the new technologies of data scanning that exist today.