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The Mouse Imaging Centre (MICe) at The Hospital for Sick Children was created as a unique resource and comprehensive imaging facility combining the latest state-of-the-art digital medical imaging technologies for the characterization of mouse functional genomics.

The goals of the Mouse Imaging Centre are:

  • To provide a variety of medical imaging technologies adapted to studying genetically modified mice. These technologies include magnetic resonance (MR) imaging, micro computed tomography (micro-CT), ultrasound biomicroscopy (UBM), and optical projection tomography (OPT).
  • To screen large numbers of mice for models of human diseases.
  • To image an individual mouse over time to observe development, disease progression and responses to experimental treatment.
  • To develop an exciting team of investigators with expertise in imaging techniques, computer science, engineering, imaging processing, developmental biology and mouse pathology.
  • To work by collaboration with researchers throughout the world.

To achieve these goals, MICe is staffed by an exciting team of investigators with expertise in imaging techniques, computer science, engineering, imaging processing, developmental biology and mouse pathology. 

If you just started working here, please visit Getting Started at MICe.



Contents

Resources

Imaging Hardware

Experimental Protocols

Image Processing

  • Magnetic Resonance Imaging (MRI).
  • Ultrasound Biomicroscopy (UBM).
  • Computed Tomography (CT).
  • Optical Computed Tomography (OPT).


Software.


Data - Atlases


Software developed at MICe:

Name

Description

RMINC

Analysis of data inside MINC volumes.

Pydpiper

Software to construct and run pipelines (image registration and otherwise)

Iterative Model Building (MBM.py)Image registration, written with the Pydpiper framework.
MAGeTCreating atlases with multiple automatically generated templates
Longitudinal registration toolsAlternate approaches to registration and analysis of longitudinal data.

minc-stuffs (formerly mice-minc-tools)

Suite of MINC tools developed at the Mouse Imaging Centre

brain-view

Visualize geometry and associated files

OPT_recon

Software to reconstruct OPT images

CT to MINCsoftware to create a 3D minc file from .tif files (microCT)
Software Tips and TricksGeneral tips and tricks on software/computer related things

Atlases.

Atlases currently under development and available for use at the Mouse Imaging Centre can be found here: Mouse Brain Atlases

Code for running the MAGeT algorithm for atlas generation is available for download. More information can be found on the MAGeT wiki page.