Neuroinformatics

For over 30 yearsBIC has been a hub for software innovation in biomedical image analysis


A Hub for Software Innovation and Data Collection

We have released and supported many reference datasets, software tools, packages and platforms over the years. Beginning with the MINC file format for imaging data, and including numerous image processing tools and pipelines, as well as databases and high performance computing clusters and grids, the BIC is a key resource for academic software development.  Our Centre shares datasets and anatomical atlases with the public and other academic and industrial partners. 


General Computing

Workstations, Computing and Data Storage

Our users are allocated a system account (currently about 350 active accounts) to access data storage space and distributed computing resources.

High Performance Computing (HPC) Queue

We provide a grid-computing cluster, composed of more than 550 CPU cores in varying memory configurations.

 

 


Data Hosting & Sharing

 

OMEGA

First open data repository fully dedicated to MEG 

BigBrain

A freely accessible, microscopic resolution 3D model of the human brain.

LORIS

LORIS (Longitudinal Online Research and Imaging System) is web-based data and project management software for neuroimaging research studies.

Box.BIC Private Cloud

A user-friendly web-based file hosting service accelerating collaboration, and helping lab members organize & consolidate their files. Box.BIC is our instance of OwnCloud, the leading open source file hosting application. 

Compute Canada

The BIC integrate storage and compute resources from Compute Canada, one of the largest research clusters in the country.  

DMP Assistant

DMP Assistant is a web-based software for preparing data management plans (DMPs). The tool follows best practices in data stewardship and walks researchers step-by-step through key questions about data management.

 


 

 

Brain Atlases

All the following adult, pediatric and non-human primate and ovine BIC atlases are available in MINC data format. Follow the links for an overview of each atlas, related methods, online visualization and downloads 


Data Processing

MINC

MINC is a flexible, multi-modal format for medical imaging data, as well as a set of programming libraries and tools for manipulating and visualizing MINC files.

CBRAIN

CBRAIN is web-based software that allows neuroimaging researchers to perform computationally intensive analyses on data by connecting them to High-Performance Computing (HPC) facilities across Canada and around the world.

Brainstorm

Brainstorm is a collaborative, open-source application dedicated to the analysis of brain recordings: MEG, EEG, fNIRS, ECoG, depth electrodes and animal invasive neurophysiology.

 

CIVET

CIVET is an image processing pipeline for fully automated volumetric, corticometric, and morphometric analysis of human brain imaging data (MRI).

Jupyter

JupyterHub brings the power of Jupyter notebooks to groups of users. It gives users access to computational environments and resources without burdening the users with installation and maintenance tasks.

VoxelStats

VoxelStats - A MATLAB package for multi-modal voxel-wise brain image analysis. Developed by the Translational Neuroimaging Laboratory.


Visualization

Plotly

Plotly's software makes it easy to create, deploy and share interactive web apps, graphs and visualizations in any programming language.

Brainbrowser

BrainBrowser is an open source JavaScript library exposing a set of web-based 3D visualization tools primarily targetting neuroimaging. 

IBIS Neuronav

IBIS (Intraoperative Brain Imaging System) is an Image-Guided Neurosurgery software platform.

xdisp

xdisp is an image display tool for X window systems developed by Bruce Pike. 

Postf

Postf is a simple display program for medical image files, originally developed by Gabriel C. Léger.

MNI ray_trace

MNI ray_trace is not interactive; it is designed for the creation of static images from the command-line.

 

JIV2

JIV2 is a register-like program written in Java. It can be used to view more than one MINC volume related through an affine transform.


Neuroinformatics Tools and Analysis

Brainweb MRI Simulator

The SBD contains a set of realistic MRI data volumes produced by an MRI simulator. These data can be used by the neuroimaging community to evaluate the performance of various image analysis methods in a setting where the truth is known.

EMMA

EMMA (Extensible MATLAB Medical image Analysis) is a toolkit designed to ease the use of MATLAB in the analysis of medical imaging data. It provides functions for reading and writing MINC files, viewing images, performing ROI operations, and performing several popular analyses.

Glim Image

glim_image performs voxel-wise analysis on MINC images as it relates to a linear model, such as VBM (Voxel Based Morphometry), to examine the changes in segmented tissue matter (white matter, gray matter, CSF), or DBM (Deformation Based Morphometry), to run statistics on the cortical atrophy.

Surfstat

Surfstat is a Matlab toolbox for the statistical analysis of univariate and multivariate surface and volumetrics data using linear mixed effects models and random field theory.

RMINC

RMNC is an R based library for Voxel Based Morphometry analysis, created by Jason Lerch in the ACELab in 2005. 

fMRIstats

fMRIstats is an fMRI statistical analysis toolkit implemented in matlab

 

NIAK

NIAK (Neuroimaging Analysis Kit) is an fMRI processing pipeline for Matlab and Octave​. 

N3

The N3 package, a part of MINC tools, implements a non-parametric method for correction of intensity non-uniformity in MRI data. Its use tends to be an essential first step in any processing sequence.

Registration Tools/ANIMAL

This family of algorithms linearly and nonlinearly register two images to each other. The most used, mritotal registers an MRI to standard Talairach space. They are all part of the MNI AutoReg package.


 

INSECT

INSECT is the algorithm to separate a structural MRI into it’s three tissue types: white matter, gray matter, and CSF.  It is available as part of the classify packages in  packages.bic.mni.mcgill.ca/.

BEAST

BEaST is a robust brain extraction method based on a multi-resolution patch-based framework. 

CANDLE

CANDLE is a Collaborative Approach for eNhanced Denoising under Low-light Excitation (CANDLE) for the processing of 3D laser scanning multiphoton microscopy images.


 

SEAL

SEAL stands for “Sulcal Extraction and Labelling” - which pretty much explains its use as well. 

 

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