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Front Neural Circuits. 2011 Feb 22;5:2. doi: 10.3389/fncir.2011.00002. eCollection 2011.

Mapping Functional Connectivity between Neuronal Ensembles with Larval Zebrafish Transgenic for a Ratiometric Calcium Indicator.

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Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University Beijing, China.


The ability to map functional connectivity is necessary for the study of the flow of activity in neuronal circuits. Optical imaging of calcium indicators, including FRET-based genetically encoded indicators and extrinsic dyes, is an important adjunct to electrophysiology and is widely used to visualize neuronal activity. However, techniques for mapping functional connectivities with calcium imaging data have been lacking. We present a procedure to compute reduced functional couplings between neuronal ensembles undergoing seizure activity from ratiometric calcium imaging data in three steps: (1) calculation of calcium concentrations and neuronal firing rates from ratiometric data; (2) identification of putative neuronal populations from spatio-temporal time-series of neural bursting activity; and then, (3) derivation of reduced connectivity matrices that represent neuronal population interactions. We apply our method to the larval zebrafish central nervous system undergoing chemoconvulsant-induced seizures. These seizures generate propagating, central nervous system-wide neural activity from which population connectivities may be calculated. This automatic functional connectivity mapping procedure provides a practical and user-independent means for summarizing the flow of activity between neuronal ensembles.


bursting activity; calcium imaging; calcium wave; chemoconvulsant; epilepsy; ratiometry; seizure; zebrafish

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