This library aim to provide integration of different libraries used for neuroscience with HPC facilities.

Currently the library is organized in 3 levels:

• Unified install and env system for all third part applications used
• Stand alone application wrappers that can be invoked by terminal or imported as a library
• Automated execution functions using ALCF Balsam

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.

What things you need to install the software and how to install them

• Neuroglancer
• CloudVolume
• Knossos Utils
• ffn
• etc

A step by step series of examples that tell you how to get a development env running

Say what the step will be

A step by step series of examples that tell you how to get a development env running

• Generate dataset Preview
• Generate dataset quality check
• Generate bad-image list

• Correct each image individually
• Correct brightness individually

• Pairwise aligment
• Global Optimzation
• Stitching

• Pairwise aligment
• Global Optimzation
• Cube rendering

• Cube cropping (removing borders)
• Cube neuroglancing
• Inset cropping

• Inset Manual annotation
• FFN compute_partitions
• FFN build_coordinates
• FFN train

• Splice data
• Inference
• Merge

• Precompute data
• Precompute Labels
• Generate Mesh

• Knossos injection/extraction
• webKnossos injection/extraction

We use SemVer for versioning. For the versions available, see the tags on this repository.

• Rafael Vescovi - Initial work
• Hanyu Li - Initial work
• Murat Keceli - Initial work
• Jeff Kinnisson - Initial work
• Bobby Kasthuri - Initial work
• Nicola Ferrier - Initial work
• Rafael Vescovi - Initial work

See also the list of contributors who participated in this project.

This project is licensed under the MIT License - see the LICENSE.md file for details

• Argonne National Laboratories
• University of Chicago
• Harvard University
• Princeton University
• Google