The Brain/MINDS Marmoset Tracer Injection image-sets.

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, 1440x1080 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)

Notes :
* 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)

Annotated electrode layouts for the animals that participated in ECoG experiments. (see https://dataportal.brainminds.jp/ecog-auditory-01 and https://dataportal.brainminds.jp/ecog-optogenetics-01)

We used auditory stimuli of different durations (AD) and frequencies (AF). In AD, 10 types of pure sinusoidal tones (1 ms rise/fall) with different durations (10, 25, 50, 75, 100, 125, 150, 175, 200, and 225 ms; 1000 Hz; 2000 stimuli in total) were randomly presented with an equal probability of 10%. In AF, 10 types of tones with different frequencies (700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500, and 1600 Hz; 50 ms; 1000 stimuli in total) were presented with an equal probability of 10%.
Epidural ECoG recordings were taken in the passive listening condition while monkeys were in awake and ketamine (30 mg/kg i.m.) administrated conditions. ECoG data were sampled at 1KHz.
Data format information can be found on TychoWiki.

The Brain/MINDS Marmoset MRI NA216 and eNA91 datasets currently constitutes the largest public marmoset brain MRI resource (483 individuals), and includes in vivo and ex vivo data for large variety of image modalities covering a wide age range of marmoset subjects.
* The in vivo part corresponds to a total of 455 individuals, ranging in age from 0.6 to 12.7 years (mean age: 3.86 ± 2.63), and standard brain data (NA216) from 216 of these individuals (mean age: 4.46 ± 2.62).
T1WI, T2WI, T1WI/T2WI, DTI metrics (FA, FAc, MD, RD, AD), DWI, rs-fMRI in awake and anesthetized states, NIfTI files (.nii.gz) of label data, individual brain and population average connectome matrix (structural and functional) csv files are included.
* The ex vivo part is ex vivo data, mainly from a subset of 91 individuals with a mean age of 5.27 ± 2.39 years.
It includes NIfTI files (.nii.gz) of standard brain, T2WI, DTI metrics (FA, FAc, MD, RD, AD), DWI, and label data, and csv files of individual brain and population average structural connectome matrices.

This atlas is composed of a population average ex-vivo MRI T2WI contrast mapped with the BMA 2017 Ex Vivo (published by Woodward et al. The Brain/MINDS 3D digital marmoset brain atlas).
The population average MRI was constructed based on scans of 25 individual brains. The 25 brains were aligned with one another by iteratively applying linear and non-linear registration and averaging the transformation files until convergence. Data of individual brains were then resampled with an isotropic spatial resolution of 100×100×100µm3 and averaged across brain. The registration procedure gave a brain shape with a high signal-to-noise ratio compared to an individual MRI scan. The average MRI was then AC-PC aligned within an RAS (Right-Anterior-Superior) coordinate system.
Cortical flat map and mid-thickness surfaces for the left and right hemispheres are now provided in the common GIFTI format (*. gii) for surface data. These are compatible with Connectome Workbench (version 1.5.0 and higher) and a Scene file is also provided for easy viewing of the data.

Eight weeks after the virus injections, we applied 3.5 V to each LED for 200 ms to monitor the development of neural responses to photostimuli. In each session, eight LEDs were pseudo-randomly illuminated and 50 stimulation trials were performed for every LED. Inter stimulus intervals were fixed at 2 s. ECoG data were sampled at 1KHz.
Further information can be found on TychoWiki

The dataset includes NifTI files of MRI T1-weighted images data and T2-weighted images at the age of 1 month, 3 months, 6 months, 12 months, 18 months, and 24 months. The templates at the age of 18 and 24 months were registered to the stereotaxic coordinates defined in Paxinos[^1] and Woodward et al[^2]. For the template at the age of 1, 3, 6, 12 months, we newly defined the stereotaxic coordinates. For details regarding the procedure, please download Additional_information_about_the_dataset.pdf

[^1]: Paxinos G. The marmoset brain in stereotaxic coordinates. Academic Press. 2012. [^2]: Woodward A, Hashikawa T, Maeda M, Kaneko T, Hikishima K, Iriki A, Okano H, Yamaguchi Y. The Brain / MINDS 3D digital marmoset brain atlas. DOI: https://doi.org/10.24475/bma.2799

The dataset includes gziped NIfTI files (.nii.gz) of MRI T2WI and DTI metrics (FA, MD, RD, and AD) in-vivo data; the ages of the data are 1,3,6,9,12,15,18 months old.
The creation process of these averaged images is referred to the script of FSL software (https://fsl.fmrib.ox.ac.uk/), fslvm_2_template, partially modified; the non-linear registration process was replaced to the script of ANTs (http://stnava.github.io/ANTs/), antsRegsitrationSyN.sh. The details are described in the text “Dataset Description and Image Processing”.
In addition, age-specific DWI templates (.mif files) are provided, which are created using the script of Mrtrix3 (http://www.mrtrix.org/), population_template. You may convert .mif file to NIFTI, extracting b-vector and b-value information by conducting the following Mrtrix3’s command: # mrconvert dwi_input.mif dwi_output.nii -export_grad_fsl bvec bval
Files can be downloaded each image type or as one zip file.

The dataset includes NIfTI files of MRI T2 ex-vivo data; reconstructed Nissl stained images of the same brain, registered to the shape of the MRI; brain region segmentation (with separate color lookup table); and gray, mid-cortical and white matter boundary segmentation. In addition, a 3D Slicer scene file is provided that can be used for testing the dataset within the freely downloadable 3D Slicer software (https://www.slicer.org/). The scene file can be dragged directly into 3D Slicer and the atlas can be used immediately. Files can be downloaded individually or as one zip file.
The atlas can be viewed online via the Zooming Atlas Viewer (ZAV) by clicking here.