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.
MICe is staffed by an exciting team of investigators with expertise in imaging techniques, computer science, engineering, imaging processing, developmental biology and mouse pathology.
At the Mouse Imaging Centre we:
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).
Use mouse models to investigate complex human disease.
Perform longitudinal phenotyping of a variety of mouse models to observe normal development, disease progression and response to experimental treatment.
We also constantly work towards:
Developing an exciting team of investigators with expertise in imaging techniques, computer science, engineering, imaging processing, developmental biology and mouse pathology.
Collaborating with researchers around the world to pursue shared scientific interests.
If you just started working here, please visit Getting Started at MICe.
Content
- Resampled Allen Brain Atlas
- Atlas to Atlas Registration with ANTS (intra or inter modality)
- brain-view
- Building a registration quarantine
- Collaboration Information
- Creating Atlases with MAGeT
- E15.5 Embryo atlas
- Experimental Protocols
- From MINC (4D) to Matlab and back
- Generating deformation fields
- ggplot2
- Home Cage Analysis
- How-to articles
- How to Upload Studies To ScanBase
- Iterative Model Building (MBM 2.0)(MBM.py)
- IVIS Lumina II bioluminescence scanner at MICe
- Longitudinal Registration Tools
- MBP Intro Statistics 2017
- MICe-build-model
- minc-stuffs (formerly mice-minc-tools)
- Mouse Brain Atlases
- Mouse Brain Imaging for Neurodevelopmental Disorders
- OPT_recon
- Optical Projection Tomography (OPT)
- Preferential Spatial Gene Expression in Neuroanatomy
- Pydpiper
- Using Pydpiper Applications
- Writing Pydpiper Code
- Pydpiper Virtual Machine
- Workflow Diagrams
- Running Pydpiper on SciNet
- Pydpiper on the SickKids HPF
- PydPiper at MICe with quarantines
- Two level registration (twolevel_model_building)
- Disk cleanup after a registration
- Pydpiper development - checklist
- Pydpiper on Graham
- Registration Quarantines (deprecated)
- Resampled Allen Atlas
- Resources
- RMINC
- Shared links
- Using MNI Register to Manually Register Volumes
- Voxelwise statistics with Batchtools
Old Home Page
Content from the home page prior to our Wiki update session on November 28th, 2019.
Software developed at MICe:
Name | Description |
|---|---|
Analysis of data inside MINC volumes. | |
Software to construct and run pipelines (image registration and otherwise) | |
| Iterative Model Building (MBM.py) | Image registration, written with the Pydpiper framework. |
| MAGeT | Creating atlases with multiple automatically generated templates |
| Longitudinal registration tools | Alternate approaches to registration and analysis of longitudinal data. |
Suite of MINC tools developed at the Mouse Imaging Centre | |
Visualize geometry and associated files | |
Software to reconstruct OPT images | |
| CT to MINC | software to create a 3D minc file from .tif files (microCT) |
| Software Tips and Tricks | General 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.