mouse-imaging-centre Goto Github PK

.github

Canonical repository for organization-wide README.md.

blog

brain-view2

cerebrovascular_analysis

classify-sklearn

MINC wrapper for python's scikit-learn for tissue/lesion/etc classification

dcm2bids-conversion

Wrapper package for dcm2bids to convert POND and KIND dicom directories to BIDS

fastcell

Fast Deep Neural Networks for Cell Image Analysis

generate_deformation_fields

Given an input Jacobian determinant, this code will generate a deformation field that produces that Jacobian field. (Made for MINC format files)

image-registration-quarantine-makefile

Provides a Makefile based on Vlad Fonov's Makefile from the EZminc package, and includes additional packages that allow you to build a full quarantine capable of image registration (geared by default to MRI mouse brain registration)

mice-apptainer

Singularity container definition for MICe/Oxford neuroimaging software

mice-lab

Scripts and pipelines that are specific to the Mouse Imaging Centre lab. These programs are not very likely to be applicable to other centres.

mice-nix-overlay

Nix expressions for installing some MINC-related medical image processing software

mice-spack-packages

Spack packages of MICe software (and some external dependencies)

minc-scripts

various scripts processing minc files or minx-associated files

minc-stuffs

Scripts and bits of code for minc files.

minc-toolkit-containers

Making containers with minc-toolkit

minc-toolkit-v2

Version 2 of the minc-toolkit, uses tools based on ITK version 4.x

minc-vm

Packer built VMs with minc-toolkit and friends

minc.jl

Julia bindings for the MINC medical imaging library (libminc2)

minc2-simple

simplified MINC2 API

minclaplace

Laplace's equation for measuring thickness (or other uses of streamlines) between two boundaries

mincmodelexplorer

mouse-imaging-book

A book detailing how do an end-to-end mouse imaging analysis

mouse-imaging-centre.github.io

Front page of the Mouse Imaging Centre

mricrotome

R package for MRI data visualization

neuronix

Use the Nix package manager to build imaging pipelines

py_minc

py_minc is a python module for working with MINC data format files, and was developed by John G. Sled.

pydpiper

Python code for flexible pipeline control

pydpiperqc

pyminc

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