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Welcome to the public wiki of the Mouse Imaging Centre.

If you are new here, the best place to start is probably here: Welcome to MICe

Software.

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.

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