open access DATA archive FUNCTIONAL MULTINEURON CALCIUMIMAGING(fMCI)
fMCI is a functional imaging technique with multicell loading of calcium
fluorophores, which was originally introduced by Yuste and Katz (Neuron
6:333-344, 1991). fMCI has unique advantages, including: i) recording en masse from hundreds of neurons in a wide area, ii) single-cell resolution, iii)
identifiable location of neurons, and iv) detection of non-active neurons
during the observation period. For details, see our review paper. Methods
Rat hippocampal slices or slice cultures were loaded with Oregon green
488 BAPTA-1AM, and calcium signals were optically recorded from the CA3
pyramidal cell layer in aCSF consisting of (in mM): 127 NaCl, 26 NaHCO3, 3.3 KCl, 1.24 KH2PO4,
1.0 MgSO4, 1.0 CaCl2 and 10 glucose. Fluorophores were excited at 488 nm and visualized with
a 507-nm long-pass emission filter. Images were captured at 10-2000 frames/s
with a Nipkow spinning-disk confocal microscope (CSU10, CSU22, and CSU-X1;
Yokogawa Electric, Tokyo, Japan), a cooled CCD camera (iXon DU860, DU897,
and DV887; Andor, Belfast, Northern Ireland, UK), an upright microscope
(ECLIPSE FN1, Nikon, Tokyo, Japan), a water-immersion objective (16X, 0.80
NA, CFI75LWD16xW, Nikon), and Metamorph software (Molecular Devices, Union
City, CA).
raw movie
ΔF/F movie
Fig. 1 Confocal movie taken from the CA3 pyramidal cell layer of a hippocampal
slice incubated in Oregon Green 488 BAPTA-1AM.
Fig. 2 Simultaneous whole-cell patch-clamp recording and calcium imaging. Action potentials (top), but not synaptc inputs, are reliably reflected in somatic calcium transients (middle), and thus, the timings of spikes can be reconstructed from the onsets of calcium transients without electrophysiologic recordings (bottom).
Data Representation
Data are given in the TEXT file format. A part of DATA_001.txt is shown below.
In this data file, the movie length is 18 min 20 sec (=11000 frames at
0.1 sec per frame). Each horizontal row in the Data part represents the
data of a single cell. This file contains 62 cells (rows). The first '
red' column indicates the cell number (assigned arbitrarily). The next two 'green' columns indicate the 'X versus Y' coordinate of the cell location (unit:
micrometer). The 'orange' number indicates the number of the total activity of the cell during the movie. For example, Cell1 showed 97 activities during the recording period of 18 min 20 sec. If
this value is zero, the neuron was silent. The following 'blue' columns indicate individual activity times of the cell, i.e., frames at which the neuron fired. For example, Cell1 was activated at frames 123, 138, 193, 260, ..., that is, it fired at 12.3, 13.8, 19.3, 26.0, ..., sec after the beginning of the movie.
As a result, the cell map and the activity rastergram can be reconstructed
from DATA_001.txt as follows.
Archive (for download, right-click on the filename)
To confirm whether you correctly reconstructed spike trains from these
data, the Visual Basic program Raster_Reconstractor.exe (76 kb) may be useful (see below). Because this program is written in Visual Basic
6.0 for Microsoft Windows PCs, VB6 runtime is required to run it. The runtime
is distributed at Microsoft Download Center (free).
References
Ikegaya, Y., Aaron, G., Cossart, R., Aronov, D., Lampl, I., Ferster, D.,
and Yuste, R. Synfire chains and cortical songs: Temporal modules of cortical
activity. Science, 304:559-564, 2004.
Sasaki, T., Kimura, R., Tsukamoto, M., Matsuki, N., Ikegaya, Y. Integrative
spike dynamics of rat CA1 neurons: a multineuronal imaging study. J. Physiol.,
574:283-290, 2006.
Sasaki, T., Matsuki, N., Ikegaya, Y. Metastability of active CA3 networks.
J. Neurosci., 27:517-528, 2007.
Takahashi, N., Sasaki, T., Usami, A., Matsuki, N., Ikegaya, Y. Watching
neuronal circuit dynamics through functional multineuron calcium imaging
(fMCI). Neurosci. Res., 58:219-225, 2007. (Link)
Note
Although these files can be freely downloaded for analysis, we still own
the copyright of the original (not analyzed) data and may claim coauthorship
when the analyzed data are published elsewhere. If you have any questions,
see contact details below.
Yuji IKEGAYA
Laboratory of Chemical Pharmacology,
Graduate School of Pharmaceutical Sciences,
The University of Tokyo.
7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
TEL: 03-5841-4783, FAX: 03-5841-4786
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