Computational methods and challenges for large-scale circuit mapping

Helmstaedter, M., Mitra, P. P. (February 2012) Computational methods and challenges for large-scale circuit mapping. Current Opinion in Neurobiology, 22 (1). pp. 162-169. ISSN 09594388 (ISSN)

URL: http://www.ncbi.nlm.nih.gov/pubmed/22221862
DOI: 10.1016/j.conb.2011.11.010

Abstract

The connectivity architecture of neuronal circuits is essential to understand how brains work, yet our knowledge about the neuronal wiring diagrams remains limited and partial. Technical breakthroughs in labeling and imaging methods starting more than a century ago have advanced knowledge in the field. However, the volume of data associated with imaging a whole brain or a significant fraction thereof, with electron or light microscopy, has only recently become amenable to digital storage and analysis. A mouse brain imaged at light-microscopic resolution is about a terabyte of data, and 1mm 3 of the brain at EM resolution is about half a petabyte. This has given rise to a new field of research, computational analysis of large-scale neuroanatomical data sets, with goals that include reconstructions of the morphology of individual neurons as well as entire circuits. The problems encountered include large data management, segmentation and 3D reconstruction, computational geometry and workflow management allowing for hybrid approaches combining manual and algorithmic processing. Here we review this growing field of neuronal data analysis with emphasis on reconstructing neurons from EM data cubes. © 2012.

Item Type: Paper
Uncontrolled Keywords: algorithm anisotropy brain mapping computer analysis confocal microscopy data analysis geometry image processing image reconstruction nerve cell network neuroanatomy neurobiology neuroimaging nonhuman perikaryon priority journal process optimization reliability review scanning electron microscopy three dimensional imaging transmission electron microscopy
Subjects: organs, tissues, organelles, cell types and functions > organs types and functions > brain
organs, tissues, organelles, cell types and functions > cell types and functions > cell types
organs, tissues, organelles, cell types and functions > cell types and functions > cell types
organs, tissues, organelles, cell types and functions > cell types and functions > cell types

organs, tissues, organelles, cell types and functions > cell types and functions
organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons > neuronal circuits
organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons > neuronal circuits
organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons > neuronal circuits

organs, tissues, organelles, cell types and functions > organs types and functions
organs, tissues, organelles, cell types and functions
CSHL Authors:
Communities: CSHL labs > Mitra lab
Depositing User: Matt Covey
Date: February 2012
Date Deposited: 30 Jan 2013 20:34
Last Modified: 30 Jan 2013 20:34
PMCID: PMC3406305
Related URLs:
URI: http://repository.cshl.edu/id/eprint/26957

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