Table of contents for all documentation

All documentation for the UCSD Active Brain Atlas project is stored in Github under this location. The documents are split between User and Programmer.

User documentation

CZI refers to the format of scanned images generated by the Zeiss scanning microscope

Neuroglancer is a visualization and annotation tool designed for large collections of scanned brain sections.

1. A description of the CZI to Neuroglancer process with detailed instructions
2. HOWTO run the entire CZI to Neuroglancer process process with step by step instructions
3. Neuroglancer
   1. Neuroglancer help for end users
   2. Adding annotation layers

Programmer documentation

1. A high level design of all our projects
2. A glossary of terms we use
3. Annotations
   1. A description of the annotation process
4. Classes
   1. Atlas class
   2. Cell dectector class
   3. Django class
   4. Pipeline class
5. Database documentation
   1. A list of the database tables
   2. Current database information being used by the REST API with Neuroglancer
6. Django documentation
   1. Releasing a new version of Django on the web server
   2. Running tasks in the background with Supervisord
   3. Creating and running unit tests for Django REST
   4. Using authentication with Django/Rest
7. Neuroglancer documentation
   1. Doing QC on an image stack in Neuroglancer
   2. Affine transformation with a description of Yuncong's process
   3. Neuroglancer technical documentation by Junjie
8. Preprocessing pipeline
   1. A high level overview of the preprocessing pipeline
   2. Setting up the software and installation for running the preprocessing pipeline
   3. The original Yuncong Elastix parameter map