Calcium Imaging - Okano 01 (DataID: 5575)
Authors: Takahiro Kondo1,2, Risa Saito3, Masaki Otaka3, Kimika Yoshino-Saito1,4, Akihiro Yamanaka5, Tetsuo Yamamori6, Akiya Watakabe6, Hiroaki Mizukami7, Mark J. Schnitzer8,9,10, Kenji F. Tanaka2,11, Junichi Ushiba12,13*, Hideyuki Okano1,2*
*corresponding authors: Junichi Ushiba (firstname.lastname@example.org), Hideyuki Okano (email@example.com)
This dataset contains neuronal population activity data recorded during naturalistic behavior of common marmosets. Calcium imaging data was collected with a miniature microscope in the motor cortex of two common marmosets (identified by letters M and W).
3 types of data are available for download :
1. raw microendoscope data (multi-tiff files, 1440×1080 pixels resolution at 20Hz sampling rate. Files are divided in 4GB segments)
2. individual cell activity time series, extracted from raw data (CSV files)
3. regions of interest (ROI) of the extracted cells (png image files)
* we analyzed all imaging data using Mosaic provided by Inscopix (Inscopix Data Processing Software, IDPS) following the "Recommended workflow" (https://support.inscopix.com/mosaic-workflow) except for acquisition-specific artifacts.
* PCA-ICA was used as the cell identification algorithm, and a serial number was affected to each identified cell (starting from 0). Before cell identification, spatial downsampling, motion correction, and df/F were applied.
* In traces.csv file, the first column indicates the time (in seconds), from the second column onward, each column represents the time series signal of each cells sorted by their serial numbers (i.e. the second column corresponds to cell #0, the third column corresponds to cell #1, and so on).
* A low-pass filter was applied to each time series signal.
* For the ROI image files (contained in th0.9.zip archive), the cell serial number is indicated in the file name (between
th0.9 prefix and
.png extension), but note that 0 is omitted for the first file (i.e.
th0.9.png corresponds to cell #0,
th0.91.png to cell #1, and so on)
Kondo, Takahiro; Saito, Risa; Otaka, Masaki; Yoshino-Saito, Kimika; Yamanaka, Akihiro; Yamamori, Tetsuo; Watakabe, Akiya; Mizukami, Hiroaki; Schnitzer, Mark J.; Tanaka, Kenji F.; Ushiba, Junichi; Okano, Hideyuki : Marmoset Calcium Imaging Dataset – Okano 01 (DataID: 5575)
Takahiro Kondo, Risa Saito, Masaki Otaka, Kimika Yoshino-Saito, Akihiro Yamanaka, Tetsuo Yamamori, Akiya Watakabe, Hiroaki Mizukami, Mark J. Schnitzer, Kenji F. Tanaka, Junichi Ushiba, Hideyuki Okano (2018) Calcium Transient Dynamics of Neural Ensembles in the Primary Motor Cortex of Naturally Behaving Monkeys. Cell Reports 24:2191 DOI: https://doi.org/10.1016/j.celrep.2018.07.057
|Marmoset M||Raw microendoscope data (zipped multi-tiff files)||recording_20161007_143400.zip||
Total downloads: 23
|Data in Neurodata Without Borders Format (zipped NWB file is splitted in 2GB chunks*)||MarmosetM-part-a||
Total downloads: 11
Total downloads: 5
|Cells’ ROI (zipped png files)||th0.9.zip||
Total downloads: 6
|Marmoset W||Raw microendoscope data (zipped multi-tiff files)||recording_20161007_145231.zip|
|Data in Neurodata Without Borders Format (zipped NWB file is splitted in 2GB chunks*)||MarmosetW-part-a|
|Cells activity (CSV file)||traces.csv||
Total downloads: 8
|Cells’ ROI (zipped png files)||th0.9.zip|
*NWB files are splitted in 2GB chunks for safer download.
Part files can be joined with the following procedure:
1) Open a terminal/command window and change current directory to the folder where the downloaded files are located (one Marmoset at a time, No other files should be in the folder)
2) Then use the command for your specific platform.
Under Linux or MacOs:
cat M*.zip > Marmoset-full.zip
COPY /B M*-a.zip + M*-b.zip + M*-c.zip + M*-d.zip + M*-e.zip + M*-f.zip + M*-g.zip + M*-h.zip + M*-i.zip + M*-j.zip Marmoset-full.zip
3) Uncompress the produced archive (