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@Mouse-Imaging-Centre Mouse Imaging Centre, Hospital for Sick Children, Toronto Canada

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    38 repositories

    • RMINC

      Public
      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, J…
      statisticsfdrmixed-modelsmass-univariate-analysisr
      R
      •
      Other
      •17•23•100•2•Updated Oct 13, 2024Oct 13, 2024

    • fastCell

      Public
      Fast Deep Neural Networks for Cell Image Analysis
      Python
      •
      MIT License
      •2•1•2•2•Updated Aug 30, 2024Aug 30, 2024

    • mice-apptainer

      Public
      Singularity container definition for MICe/Oxford neuroimaging software
      0•0•4•0•Updated Aug 1, 2024Aug 1, 2024

    • minclaplace

      Public
      Laplace's equation for measuring thickness (or other uses of streamlines) between two boundaries
      Cython
      •5•8•3•0•Updated Oct 6, 2022Oct 6, 2022

    • mice-spack-packages

      Public
      Spack packages of MICe software (and some external dependencies)
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 5, 2022Oct 5, 2022

    • pydpiper

      Public
      Python code for flexible pipeline control
      Python
      •
      Other
      •10•25•151•0•Updated Sep 29, 2022Sep 29, 2022

    • .github

      Public
      Canonical repository for organization-wide README.md.
      0•0•0•0•Updated Sep 29, 2022Sep 29, 2022

    • pyminc

      Public
      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
      Python
      •
      Other
      •8•14•19•1•Updated Sep 26, 2022Sep 26, 2022

    • RMINC-test-data

      Public
      Data files for running RMINC tests
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Sep 9, 2022Sep 9, 2022

    • minc-stuffs

      Public
      Scripts and bits of code for minc files.
      Python
      •
      Other
      •5•6•25•1•Updated Apr 27, 2022Apr 27, 2022

    • minc-toolkit-v2

      Public
      Version 2 of the minc-toolkit, uses tools based on ITK version 4.x
      CMake
      •
      GNU General Public License v3.0
      •22•0•0•0•Updated Apr 25, 2022Apr 25, 2022

    • scanbaseTools

      Public
      Tools for uploading and interacting with scanbase
      R
      •
      Other
      •0•0•2•0•Updated Jan 27, 2022Jan 27, 2022

    • MICe-lab

      Public
      Scripts and pipelines that are specific to the Mouse Imaging Centre lab. These programs are not very likely to be applicable to other centres.
      Python
      •3•0•14•0•Updated Nov 24, 2021Nov 24, 2021

    • neuronix

      Public
      Use the Nix package manager to build imaging pipelines
      Nix
      •
      MIT License
      •0•0•0•0•Updated Oct 19, 2021Oct 19, 2021

    • mice-nix-overlay

      Public
      Nix expressions for installing some MINC-related medical image processing software
      Nix
      •
      MIT License
      •0•1•4•0•Updated Oct 19, 2021Oct 19, 2021

    • dcm2bids-conversion

      Public
      Wrapper package for dcm2bids to convert POND and KIND dicom directories to BIDS
      Python
      •0•0•0•0•Updated Apr 1, 2021Apr 1, 2021

    • MINC.jl

      Public
      Julia bindings for the MINC medical imaging library (libminc2)
      Julia
      •0•0•0•0•Updated Oct 19, 2020Oct 19, 2020

    • brain-view2

      Public
      C++
      •1•5•2•1•Updated Jun 23, 2020Jun 23, 2020

    • Mouse-Imaging-Book

      Public
      A book detailing how do an end-to-end mouse imaging analysis
      0•0•0•0•Updated May 20, 2020May 20, 2020

    • MINC-VM

      Public
      Packer built VMs with minc-toolkit and friends
      Shell
      •3•0•0•0•Updated Mar 17, 2020Mar 17, 2020

    • MRIcrotome

      Public
      R package for MRI data visualization
      R
      •1•3•14•0•Updated Feb 25, 2020Feb 25, 2020

    • minc2-simple

      Public
      simplified MINC2 API
      C
      •
      Other
      •2•0•0•0•Updated Nov 12, 2019Nov 12, 2019

    • tissue_vision_tools

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 8, 2019Nov 8, 2019

    • pydpiperQC

      Public
      R
      •
      Other
      •0•0•7•0•Updated May 8, 2019May 8, 2019

    • generate_deformation_fields

      Public
      Given an input Jacobian determinant, this code will generate a deformation field that produces that Jacobian field. (Made for MINC format files)
      Python
      •
      Other
      •4•2•1•0•Updated Apr 12, 2019Apr 12, 2019

    • minc-scripts

      Public
      various scripts processing minc files or minx-associated files
      Python
      •
      MIT License
      •3•0•0•0•Updated Oct 26, 2018Oct 26, 2018

    • minc-toolkit-containers

      Public
      Making containers with minc-toolkit
      Dockerfile
      •4•0•0•0•Updated Oct 11, 2018Oct 11, 2018

    • blog

      Public
      HTML
      •0•0•0•0•Updated Oct 1, 2018Oct 1, 2018

    • mincModelExplorer

      Public
      R
      •0•0•0•0•Updated Aug 14, 2018Aug 14, 2018

    • Scinet-SS-bayesian-neuroimaging-R

      Public
      Slides for the Scinet Summer School session on bayesian analysis of neuroimaging data with R and Stan
      HTML
      •1•2•0•0•Updated Jun 19, 2018Jun 19, 2018