neurodata/cloudreg repository overview

⁠CloudReg

⁠CloudReg is a tool for cross-modal, nonlinear, image registration between arbitrary image volumes.

• Overview⁠
• Documentation⁠
• System Requirements⁠
• Installation Guide⁠
• License⁠
• Issues⁠
• Citing CloudReg⁠

⁠Overview

Quantifying terascale multi-modal human and animal imaging data requires scalable analysis tools. We developed CloudReg, an automated, terascale, cloud-based image analysis pipeline for preprocessing and cross-modal, non-linear registration between volumetric datasets with artifacts. CloudReg was developed using cleared mouse and rat brain light-sheet microscopy images, but is also accurate in registering the following datasets to their respective atlases: in vivo human and ex vivo macaque brain magnetic resonance imaging, ex vivo murine brain micro-computed tomography. Our extensive documentation (below) can enable deployment of this tool for many other datasets/research questions.

⁠Documentation

The official documentation with usage is at https://cloudreg.neurodata.io⁠

Please visit the Run section⁠ in the official website for more in depth usage.

⁠System Requirements

⁠Hardware requirements

CloudReg requires only a standard computer with enough RAM to support the in-memory operations since the majority of work is run in cloud services.

⁠Software requirements

⁠OS Requirements

CloudReg is tested on the following OSes and requires Python 3:

• Linux x64
• macOS x64

⁠Installation Guide

Please see Setup⁠ on the official website for detailed set up information.

⁠License

This project is covered under the Apache 2.0 License.

⁠Issues

We appreciate detailed bug reports and feature requests (though we appreciate pull requests even more!). Please visit our issues⁠ page if you have questions or ideas.

⁠Citing CloudReg

If you find CloudReg useful in your work, please cite the tool via the CloudReg paper⁠