Mouse Imaging Centre, Hospital for Sick Children, Toronto Canada
25 Orde Street, Toronto, Ontario M5T 3H7
Pinned Repositories
brain-view2
mice-apptainer
Singularity container definition for MICe/Oxford neuroimaging software
minc-stuffs
Scripts and bits of code for minc files.
minclaplace
Laplace's equation for measuring thickness (or other uses of streamlines) between two boundaries
MRIcrotome
R package for MRI data visualization
pydpiper
Python code for flexible pipeline control
pyminc
A python interface to the MINC 2 library, allowing use of numpy arrays to access MINC data, and other such similar goodies, developed by Jason Lerch
RMINC
Statistics for MINC volumes: A library to integrate voxel-based statistics for MINC volumes into the R environment. Supports getting and writing of MINC volumes, running voxel-wise linear models, correlations, etc.; correcting for multiple comparisons using the False Discovery Rate, and more. With contributions from Jason Lerch, Chris Hammill, Jim Nikelski and Matthijs van Eede. Some additional information can be found here:
Scinet-SS-bayesian-neuroimaging-R
Slides for the Scinet Summer School session on bayesian analysis of neuroimaging data with R and Stan
summer_school2017
Mouse Imaging Summer School 2017
Mouse Imaging Centre, Hospital for Sick Children, Toronto Canada's Repositories
Mouse-Imaging-Centre/pydpiper
Python code for flexible pipeline control
Mouse-Imaging-Centre/RMINC
Statistics for MINC volumes: A library to integrate voxel-based statistics for MINC volumes into the R environment. Supports getting and writing of MINC volumes, running voxel-wise linear models, correlations, etc.; correcting for multiple comparisons using the False Discovery Rate, and more. With contributions from Jason Lerch, Chris Hammill, Jim Nikelski and Matthijs van Eede. Some additional information can be found here:
Mouse-Imaging-Centre/pyminc
A python interface to the MINC 2 library, allowing use of numpy arrays to access MINC data, and other such similar goodies, developed by Jason Lerch
Mouse-Imaging-Centre/minclaplace
Laplace's equation for measuring thickness (or other uses of streamlines) between two boundaries
Mouse-Imaging-Centre/minc-stuffs
Scripts and bits of code for minc files.
Mouse-Imaging-Centre/brain-view2
Mouse-Imaging-Centre/MRIcrotome
R package for MRI data visualization
Mouse-Imaging-Centre/generate_deformation_fields
Given an input Jacobian determinant, this code will generate a deformation field that produces that Jacobian field. (Made for MINC format files)
Mouse-Imaging-Centre/Scinet-SS-bayesian-neuroimaging-R
Slides for the Scinet Summer School session on bayesian analysis of neuroimaging data with R and Stan
Mouse-Imaging-Centre/fastCell
Fast Deep Neural Networks for Cell Image Analysis
Mouse-Imaging-Centre/mice-nix-overlay
Nix expressions for installing some MINC-related medical image processing software
Mouse-Imaging-Centre/mice-apptainer
Singularity container definition for MICe/Oxford neuroimaging software
Mouse-Imaging-Centre/MICe-lab
Scripts and pipelines that are specific to the Mouse Imaging Centre lab. These programs are not very likely to be applicable to other centres.
Mouse-Imaging-Centre/neuronix
Use the Nix package manager to build imaging pipelines
Mouse-Imaging-Centre/.github
Canonical repository for organization-wide README.md.
Mouse-Imaging-Centre/blog
Mouse-Imaging-Centre/dcm2bids-conversion
Wrapper package for dcm2bids to convert POND and KIND dicom directories to BIDS
Mouse-Imaging-Centre/mice-spack-packages
Spack packages of MICe software (and some external dependencies)
Mouse-Imaging-Centre/minc-scripts
various scripts processing minc files or minx-associated files
Mouse-Imaging-Centre/minc-toolkit-containers
Making containers with minc-toolkit
Mouse-Imaging-Centre/minc-toolkit-v2
Version 2 of the minc-toolkit, uses tools based on ITK version 4.x
Mouse-Imaging-Centre/MINC-VM
Packer built VMs with minc-toolkit and friends
Mouse-Imaging-Centre/MINC.jl
Julia bindings for the MINC medical imaging library (libminc2)
Mouse-Imaging-Centre/minc2-simple
simplified MINC2 API
Mouse-Imaging-Centre/mincModelExplorer
Mouse-Imaging-Centre/Mouse-Imaging-Book
A book detailing how do an end-to-end mouse imaging analysis
Mouse-Imaging-Centre/pydpiperQC
Mouse-Imaging-Centre/RMINC-test-data
Data files for running RMINC tests
Mouse-Imaging-Centre/scanbaseTools
Tools for uploading and interacting with scanbase
Mouse-Imaging-Centre/tissue_vision_tools