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Scaffold Mapping Tools

SPARC's scaffold mapping tools enable users to map data onto anatomical organ scaffolds.

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Introduction

The MAP-Core scaffold mapping tools enable users to robustly and reproducibly map SPARC data onto anatomical organ scaffolds. The scaffold mapping tools will also ensure that required metadata and visualization files are correctly added to a dataset to enable rendering and visual exploration on the SPARC Portal.

The MAP-Core scaffold mapping tools is a specialized release of the MAP-Client application which is a framework for managing workflows. The specialized release is prepackaged with the tools required for mapping data to organ scaffolds, producing visual renderings for the SPARC Portal, and enriching datasets with the mapped data.

Detailed documentation for the MAP Client is available, but here we focus on how to use the scaffold mapping tools to map data to scaffolds in the MAP Client environment.

Download

The latest version of the mapping tools is available to download here:

Windows

Mapping tools v0.21.4 - latest version

The download above is a Windows application installer for a 64-bit architecture. Installation instructions for which are available here

Previous releases

Demonstration

The documentation of the MAP-Core scaffold mapping tools comprises a large amount of text. Reading such a large amount of text is prohibitive to a person looking to map data to a scaffold. The MAP-Core scaffold mapping tools documentation is better used for reference when looking to bring additional capabilities into play. A demonstration of how data is mapped to a scaffold is, possibly, a better way to introduce new users to the MAP-Core scaffold mapping tools.

There are three mapping demonstrations that a user may choose to follow, you are free to choose the most appropriate one for your own requirements.

  1. Mapping Image Data
    This documentation will take a user through the complete process of taking data that is to be mapped to a scaffold, all the way through to a SPARC dataset that is ready to be published on the SPARC portal, complete with interactive visualization.
  2. Mapping Physiological Data
    This documentation will take a user through the complete process of mapping cell density to a scaffold.
  3. Mapping Image Data From Flat Preparation
    This documentation will take a user through the complete process of mapping segmented flat mount data to a scaffold.

Mini-Demonstrations

The following are mini-demonstrations on a particular feature not discussed in the above demonstrations but useful when working with your own data.

  1. Adding fiducial markers and groups

Contributing

The MAP Core scaffold mapping tools is an open-source software project and welcome additions, suggestions, and feedback. To contribute simply go to Mapping Tools and leave a message, or start a pull request.

Updated 4 months ago

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