Scaffold Mapping Tools: Mapping Image Data Demonstration Overview

In this demonstration, we are going to work through how to map data onto an organ scaffold and prepare a dataset that is ready to publish on the SPARC Portal. To achieve this we are going to use the latest version of the scaffold mapping tools and a segmentation of part of the neural network from the colon of a mouse.

The latest release of the scaffold mapping tools incorporates the latest scaffolds and tools for curating SPARC datasets. We have also included some improvements to the user interface and bug fixes.

• Download the segmentation data to embed in the scaffold.
• Download the latest scaffold mapping tool version.
• Install the MAP Scaffold Mapping Tool application by following installer instructions.

After installation of the scaffold mapping tools, we need to create a skeleton SPARC dataset. We will add the data we are going to map into the skeleton dataset just as we would if we were creating a dataset that we intended to publish on the SPARC Portal.

Once the dataset is ready we will embed the segmentation data into an organ scaffold and generate the visualization files required for rendering the embedded data and scaffold on the SPARC Portal.

The result of this demonstration will be a SPARC dataset containing the original data, the files necessary for the visualization of the resultant scaffold map, and annotations that provide supplemental contextual information. This SPARC dataset will be ready to begin the publication process onto the SPARC portal.

Move on to Creating the Dataset Structure or return to the main MAP-Core Scaffold Mapping Tools page.