PICSL Histology Annotation Server

Contents:

• About PHAS
• Quick Start
  • Prerequisites
  • Install PHAS
  • Configuration and Launching
  • Creating Users, Projects and Tasks
• Organizing Histology Data
  • Prerequisites
  • Data Organization Overview
  • Archive Organization
  • Preprocessed Data
  • Project Descriptor Json
• Permission Model
  • Access Levels
  • Project-Level vs Task-Level Permissions
  • Permission Precedence
  • Examples
  • Setting Permissions
  • Security Considerations
• Histology in Google Cloud Storage
  • Obtaining and Using a GCP Key
  • Project Descriptor Json
• Running in a Production Environment
  • Installing Required Packages
  • Configuring NGINX
  • Configuring UWSGI
  • Run the Slide Server as a systemd Service
• Upgrading
  • Before Upgrading
  • Instructions for Specific Releases
  • Generic Instructions
• Notes: Tanglethon Validation
  • Create a new task for validation
  • Generate actual samples at random from curves
• PHAS Client API Reference
  • Usage Examples
  • API Reference

The PICSL Histology Annotation Server (PHAS) is a platform for visualizing and annotating large serial histology datasets via the web. It allows annotation to be easily crowdsourced with a centralized data repository.

Indices and tables

• Index

• Module Index

• Search Page