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New software tool to advance neuroscience

Researchers at the UPM and CSIC, members of the Cajal Blue Brain project, develop ESPINA, a new freeware software tool for studying the brain structure in greater depth.

Noticia. Enviado por prensa válido desde 10/11/2011 hasta 10/12/2011 (caducado)

10 November 2011. ESPINA will help to explore new hypotheses in order to improve our understanding of the human brain or look for new solutions to fight diseases such as Alzheimer's, epilepsy and Parkinson's.

As a result of Cajal Blue Brain project research, researchers at CeSViMa (Facultad de Informática, CTB) and CSIC (Laboratorio Cajal de Circuitos Corticales) have developed ESPINA, a freeware software tool for gathering new information about brain structure. From three-dimensional images output by an electron microscope, the expert can semi-automatically analyze different structures present in 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 results (1, 2) have been published in scientific journals and reported at international conferences.

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

ESPINA is implemented using the Python programming language and is designed using free distribution tools, such as Qt for GUI development, VTK for displaying three-dimensional data or ITK for image processing.  This way it can be distributed freely. ESPINA is a multiplatform tool and operates on computers running Linux or Windows.

Taking into account the singular nature of the data that is able to process as well as the implemented functionality, this software tool is without comparison today. Thanks to ESPINA, experts have analysed the available data much faster using the new data scanning technologies existing today.



1. Morales, J; Alonso-Nanclares, L; Rodríguez, JR; Merchán-Pérez, A; Defelipe, J; Rodríguez, A. Fast interactive quantification of synapses in the cerebral cortex. International Journal on Artificial Intelligence Tools 20 (2) Sp. Iss. SI: 239-252. 2011

2. Morales, J; Alonso-Nanclares, L; Rodríguez, JR; Defelipe, J; Rodríguez, A.; Merchán-Pérez, A, ESPINA: a tool for the automated segmentation and counting of synapses in large stacks of electron microscopy images. Frontiers in Neuroanatomy 5 (18) SI: 1-8. 2011


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