Databases & Tools

Ongoing assignment and its progress

Databases

Degu-3D atlas
Degu-3D atlas
<Summary>

The Caviomorph rodent degu (Octodon degu) is a novel rodent model for researches of higher cognitive brain function. Their social systems are unique and quite different from those of rats and mice. The diurnal degus live in tight-knit, extended family unit with complicated social behaviors, such as vocal communications. Furthermore, we demonstrated that Degu can be trained to use a tool, T-shaped rake. This project aims to create the world’s first digital 3-D brain atlas of Degu, comprising of combined histological and MR images.

<Contact Information>

Lab. for Symbolic Cognitive Development (Atsushi Iriki iriki(at)brain.riken.jp)

<URL>

http://brainatlas.brain.riken.jp/degu/modules/xoonips/listitem.php?index_id=24

Marmoset-3D atlas
Marmoset-3D atlas
<Summary>

Common Marmoset (Callithirix jacchus) is a novel primate model animal with transgenic line. Common Marmoset is a small new world primate that, because of its size, availability, and unique biological characteristics, has attracted considerable attention as a potentially useful biomedical research animal in fields such as neuroscience, stem cell research, drug toxicology, immunity and autoimmune diseases, and reproductive biology. This project aims to create the world’s first digital 3-D brain atlas of Marmoset, comprising of combined histological and MR images.

<Contact Information>

Lab. for Symbolic Cognitive Development (Atsushi Iriki iriki(at)brain.riken.jp)

<URL>

http://brainatlas.brain.riken.jp/marmoset/modules/xoonips/listitem.php?index_id=66   <NEW>

Marmoset-the MRI Standard brain
Marmoset-the MRI Standard brain
<Summary>

The common marmoset (Callithrix jacchus), a small New World primate species, has been widely used in neuroscience research, to which voxel-wise statistics could be extended with a species-specific brain template. We have constructed, for the first time, a tissue-segmented, population-averaged standard template of the common marmoset brain.

<Contact Information>

Lab. for Symbolic Cognitive Development (Atsushi Iriki iriki(at)brain.riken.jp)

<URL>

http://brainatlas.brain.riken.jp/marmoset/modules/xoonips/listitem.php?index_id=71

Japanese Macaque Monkey-the MRI standard brain
Japanese Macaque Monkey-the MRI standard brain
<Summary>

Japanese macaque monkey (Macaca fuscata) has been widely used in neuroscience research, including studies of higher cognitive brain functions. We have constructed, for the first time, standard MRI template of its brain. The template is useful for spatially normalizing Japanese macaque brains into a standard space, and voxel-based quantitative techniques.

<Contact Information>

Lab. for Symbolic Cognitive Development (Atsushi Iriki iriki(at)brain.riken.jp)

<URL>

http://brainatlas.brain.riken.jp/jm/modules/xoonips/listitem.php?index_id=9

BrainTx (Former CDT-DB)
BrainTx (Former CDT-DB)
<Summary>

The Brain Transcriptome Database (BrainTx) project aims to create an integrated platform to visualize and analyze our original transcriptome data and publicly accessible transcriptome data related to the genetics that underlie the development, function, and dysfunction stages and states of the brain. BrainTx was developed from the Cerebellar Development Transcriptome Database (CDT-DB). The support from BSI-NI Fund for this platform has ended in 2011. It is continuously managed as the INCF Japan Node platform by the chairman Dr. Furuichi, from Tokyo University of Science.

* INCF Japan Node Platform

<Contact Information>

Tokyo University of Science (Teiichi Furuichi tfuruichi(at)rs.tus.ac.jp)

<URL>

http://www.cdtdb.neuroinf.jp/

Neurotycho
Neurotycho
<Summary>

Project Tycho is named after Tycho Brahe. The project aims to share reliable massive neural and behavioral data for understanding brain mechanism. The dataset was recorded and distributed by Laboratory for Adaptive Intelligence, BSI, RIKEN. It is not only for neuroscientists but for everyone who is interested in learning neural mechanism.

<Contact Information>

Lab. for Adaptive Intelligence (Naotaka Fujii contact(at)neurotycho.org)

<URL>

http://neurotycho.org/

CelLoc-3D
CelLoc-3D
<Summary>

CelLoc-3D is a database of the 3D arrangement of neocortical cells (gultamatargic/excitatory, GABAergic/inhibitory and/or astrocytes) identified in vivo in layer 2/3 of the primary visual cortex of the mouse by two-photon imaging. Users can construct and download their own dataset by choosing the parameters of 1) the age of the mice, 2) the size of the imaging volume, and 3) the number of each type of cells included in the volume. We will provide 3D arrangements of the cells after the results are published. Additional data will be added when they are ready to open to the public.

<Contact Information>

Laboratory for Cortical Circuit Plasticity (Ebina, Tsumoto teppei-ebina(at)brain.riken.jp, tsumoto(at)brain.riken.jp)

<URL>

http://celloc3d.brain.riken.jp/

Mathematical Neuroscience
Mathematical Neuroscience
<Summary>

Mathematical neuroscience searches for fundamental principles of information processing by using simples models of neural networks through mathematical analysis, although the brain has found the same principles through a long history of evolution. The current project is a historical one, integrating published and unpublished papers towards establishment of mathematical neuroscience.

<Contact Information>

( )

<URL>

https://bsi-ni.brain.riken.jp/modules/page/index.php?content_id=9

The Autism CNV database
The Autism CNV database
<Summary>

Autism spectrum disorder (ASD) is a severe early onset nerurodevelopmental disorder characterized by social impairments and communication difficulties. Recent studies have demonstrated that copy number variation (CNV), either duplication or deletion of a section of DNA with a length usually from 1 kb to several Mb, are critical pathogenic factors to ASD. Given the heterogeneity and complexity of the CNV data, it remains challenging to understand how CNV contributes to ASD and why same CNV may give rise to different phenotypes. Here we present a high-quality ASD CNV database, which is based on manually curated information from literatures and Japanese ASD individuals. In addition, we also enable visualization of complex CNV data and also provide human to mouse synteny maps for CNVs, which is particularly relevant to animal studies. We hope this database will be a useful resource to tackle the genetic complexity of ASD and also can help clinicians for better diagnoses and caring for ASD individuals.

<Contact Information>

The Autism CNV database (Hiroaki Mutsumine hiroaki.mutsumine(at)riken.jp)

Tools

Multichannel EEG data for Brain Machine Interface (BMI) and/or Human Emotions (HE)
Multichannel EEG data for Brain Machine Interface (BMI) and/or Human Emotions (HE)
<Summary>

Main objective is to develop software (algorithms) for analysis of multidimensional brain data, especially multichannel EEG data. Multi-way array (tensor) factorizations and decompositions have emerged as new tools with a wide range of important potential applications, including bioinformatics, brain computer interface (BCI), text mining, image understanding and classification. We will provide experimental raw EEG data for BCI and classification of human emotions. The experimental brain data will be systematically upgraded depending on progress in recording and analyzing new brain data.

EMOTIONS CLASSIFICATION USING EEG DATA  <NEW>

<Contact Information>

Lab. for Advanced Brain Signal Processing (Andrzej Cichocki a.cichocki(at)riken.jp)

<URL>

https://bsi-ni.brain.riken.jp/modules/page/index.php?content_id=6

EToS (Efficient Technology of Spike-Sorting)
EToS (Efficient Technology of Spike-Sorting)
<Summary>

Extra-cellularly recorded signals by single or multi electrodes contain the spike events of a number of adjacent or distant neurons. Spike-sorting methods are techniques to sort detected multi-unit activities into spike trains of individual neurons and important step for analysis of multi-neuron activities. "EToS" is a high performance spike-sorting system using latest technologies concerned with signal processing and machine learning and can accurately sort spikes into many neurons. Programs in EToS are all parallelized using OpenMP and efficiently calculate on the computers with multi-core processors.

<Contact Information>

Lab. for Neural Circuit Theory (Takashi Takekawa takekawa(at)users.sourceforge.net)

<URL>

http://etos.sourceforge.net/

MGL - matlab package for displaying visual psychophysics stimuli
MGL - matlab package for displaying visual psychophysics stimuli
<Summary>

Mgl is a suite of mex/m files for displaying visual psychophysics stimuli and writing experimental programs in Matlab. Runs on Mac OS X (G4/5 and Intel 32 and Intel 64 bit OS Versions 10.5-10.7) Version 2.0. An older version 1.5 runs on Linux.

<Contact Information>

Gardner Research Unit (Justin L. Gardner jlg(at)stanford.edu)

<URL>

http://gru.stanford.edu/doku.php/mgl/overview

mrTools - matlab package for analyzing fMRI data
mrTools - matlab package for analyzing fMRI data
<Summary>

mrTools provides a set of Matlab tools to analyze fMRI data. It can do basic analyses like correlation analyses used in retinotopy experiments, event-related and GLM analyses. It can display the results of analyses on inplane anatomies, flat maps and surfaces. It is designed to make it easy to write your own script and programs in Matlab to analyze your data.

<Contact Information>

Gardner Research Unit (Justin L. Gardner jlg(at)stanford.edu)

<URL>

http://gru.stanford.edu/doku.php/mrTools/overview

Two-Color Bioarray Analysis
Two-Color Bioarray Analysis
<Summary>

"Two-Color Bioarray Analysis Software" for Gene Expression analysis using the microarray "3D-Gene" (Toray Industries, Inc.) developed by the RRC is capable of detecting gene expression differences in 2 samples using a scatter plot.

<Contact Information>

RRC/BMA (Bioarray Staff RRC-Bioarray(at)brain.riken.jp)