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Welcome to the public wiki of the Mouse Imaging Centre.

Software.

Software developed at MICe:

Name

Description

RMINC

Analysis of data inside MINC volumes.

MAGeTCreating atlases with multiple automatically generated templates
Longitudinal registration toolsAlternate approaches to registration and analysis of longitudinal data.
Pairwise nonlinear registrationPairwise nonlinear registration of a number of input volumes. A potential alternative to the MICe-build-model pipeline.

minc-stuffs (formerly mice-minc-tools)

Suite of MINC tools developed at the Mouse Imaging Centre

MICe-build-model

Iterative registration to create a consensus average of a set of MRIs

brain-view

Visualize geometry and associated files

Pydpiper

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

OPT_recon

Software to reconstruct OPT images

ct_to_mincsoftware to create a 3D minc file from .tif files (microCT)

Atlases.

Atlases developed at the Mouse Imaging Centre can currently be found here: http://www.mouseimaging.ca/technologies/mouse_atlas.html

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.

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