SPARC vocabulary services

This is available only for SPARC researchers.

The Welcome dialog is displayed when you open a file so that you can gain access to the SciCrunch database to retrieve anatomical terminology lists (or parcellation lists) compliant with FAIR data principles.

Input Subject information about the image and select the Criteria for anatomic termsfrom the drop-down menus (see descriptions under Settings below) then click Begin to:

  • Open the image and save the Subject information metadata to your data file.
  • Retrieve an anatomical terminology list, compliant with FAIR data principles, corresponding to the criteria you specified. The anatomical terms (SPARC terms) will be available in the list of contour, marker, and vessel names that you can use for annotation (segmentation).
  To modify your subject metadata or access another list of anatomic terms from SciCrunch during the session, click the SPARC vocabulary services button in the Trace ribbon bar.
  To update a data file with the most recent anatomic terms from the SciCrunch database, click the Link Terms button.
  To update multiple data files with the most recent anatomic terms from the SciCrunch database, click the Batch button.

 

To enable this functionality, you need to obtain an API key from SciCrunch that you will use in Neurolucida 360.

  1. Go to https://scicrunch.org/ and click Register in the top menu.
  2. Fill out the registration form to create an account.
  3. From "My account", click API keys.
  4. Click Generate an API key.
  5. Copy the key. You will paste it into Neurolucida 360.
  6. Return to Neurolucida 360 and paste the key in the dialog, then click Set API key.

    Right-click and select Paste. Ctrl-V doesn't work.

Subject information:

  • Select the specimen Species from the drop-down menu.

  • Type in the Subject ID

  • Choose the Sex of the specimen. Note the "blinded to condition" option.

  • Type in the Age of the animal and choose units for the age from the drop-down menu.

Species, subject ID, sex, and age are metadata that will be stored to the XML data file. They are independent from the criteria for anatomic terms selected.

Select criteria for anatomic terms:

Use the drop-down menus to select the following.

  • ORGAN: The organ you annotating.
  • SPECIES: The species you want to use for annotation.
  • PARCELLATION: The atlas parcellation scheme you want to use for annotation. If you don't see the correct parcellation, select Species Independent.

 

Learn more about FAIR data