Map data to the scaffold.
Open the scaffold mapping tool and start the sparc-data-mapping workflow. Note that a step-by-step guide on how to use the scaffold mapping tool is available here. This protocol requires version v0.17.2 or newer of the scaffold mapping tools. This document will instead focus on the specific items that need to be checked during the workflow process: a) Selecting the data file: Ensure the correct MBF XML file is used as the input file under the MBFXMLFile plugin.
b) Selecting a scaffold: Check that you have selected the correct organ and species scaffold.
c) Fitting the scaffold to data
i) Inspect the data and check that it corresponds to the image data.
ii) Under Model coordinates, make sure you select the correct coordinates that best describe the configuration of the organ when the data sample was prepared. For instance, if the data was derived from a flat preparation, select “flat coordinates”. If the data was a biopsy from an intact organ or imaging of a whole organ, select “coordinates”.
iii) After performing the fit, check that every part of the data has been fitted to the correct scale and the data is in the correct location on the scaffold and is complete before proceeding to the next step.
d) Creating a visualization of data embedded on the scaffold
i) After setting up the visualization of the scaffold and the embedded data, have a visual inspection to make sure that the embedded data is at the expected location of the scaffold. The visualization should convey an adequate representation of the spatial orientation of the embedded data with respect to the scaffold.
ii) Check that the embedded data is complete and there are no missing parts.
iii) Check that the embedded data is not obscured by any surfaces of the scaffold.
iv) Check that the graphics (surface, lines, points, contours) are assigned to the correct subgroups.
v) If certain annotations are to be displayed in the legend on the portal, make sure the graphics for those annotations have been created and assigned to the correct sub-groups.
vi) Create different views to capture essential features of the scaffold map so that the details can be presented to portal users.
vii) Context card - Use context card annotation functionality in the scaffold mapping tool to populate information for displaying contextual information for the scaffold map on the SPARC portal. Information includes a heading title for the context card, followed by a short and comprehensive description illustrating what is depicted on the scaffold map. Use the tool to add a contextual annotation for each sample mapped onto the scaffold. This will allow each sample to be linked to their DOI (if the sample came from a different dataset), the path to the sample data file in the dataset, their unique identifiers, and the specific view created for highlighting the mapped sample on the scaffold. Information about the sample (for example, what does the blue dots or color field represent) can be entered into the description field to provide the portal users with more context of the legend. Lastly, use the tool to annotate each of your created views to link them back to corresponding samples. We can also add physiological annotations (UBERON identifiers etc.) to apply to a sample or view, which will enhance the findability of the item.