ABI Mapping Tools

The ABI Mapping Tools are a collection of software tools to support the mapping of data onto scaffolds.

Overview

The ABI Mapping Tools is comprised of a large collection of disparate software packages. In general the mapping tools are split into a user interface (UI) and enginei (a software library). The UI for mapping tools are provided as plugins for MAP Client. The engines for mapping tools are standard Python packages that can be installed and utilised independently from the UI.

MAP Client

The Musculoskeletal Atlas Project Client (MAP Client) is an open-source cross-platform framework for managing workflows. A workflow, as far as MAP Client is concerned, consists of a number of connected workflow steps. The MAP Client framework is a plugin-based application where the plugins are workflow steps. MAP Client is a Python based application which makes use of the Qt widget library.

Documentation for the project can be found at MAP Client documentation.

MAP Client is available to download from MAP Client download. It is also available from PyPI.org, where you can install it with pip: pip install mapclient.

To get the best out of the MAP Client you will need to get some plugins. A collection of available plugins can be found at MAP Client plugins.

UI Documentation

This section of the documentation covers the user interface plugins used in MAP Client.

• Scaffold Creator
• Geometry Fitter
• Data Embedder
• Field Fitter
• MAP Client Plugin - SPARC Curation Helper
• Argon Viewer Step
• MAP Client Plugin - Merge Zinc Data
• MAP Client Plugin - Convert Coordinate Field

The following are MAP Client plugins that only require configuration and have no user interface.

• MAP Client Plugin - Argon Scene Exporter
• MAP Client Plugin - Convert Data to Zinc
• MAP Client Plugin - Dict Serializer
• MAP Client Plugin - Directory Chooser
• MAP Client Plugin - File Chooser
• MAP Client Plugin - File Location Sink
• MAP Client Plugin - MAP Client Provenance Record
• MAP Client Plugin - MBF XML 2 Ex Converter
• MAP Client Plugin - Muxer
• MAP Client Plugin - Save Argon Document
• MAP Client Plugin - Multiple File Chooser

Library Documentation

This section of the documentation covers the libraries used behind the user interfaces.

• scaffoldmaker library
• scaffoldfitter library
• dataembedder library
• fieldfitter library
• OpenCMISS-Argon
• OpenCMISS Exporter
• OpenCMISS Importer
• OpenCMISS Maths
• OpenCMISS Utils
• OpenCMISS ZincWidgets
• SPARC Curation Tools
• OpenCMISS-Zinc library

Funding Agencies

The National Institutes of Health (NIH) have provided the funding for this work through the SPARC project.

Contributing Organisations

The Auckland Bioengineering Institute (ABI) has contributed to this work.