This page outlines how SPARC investigators can access curated vocabulary terminology in MBF Bioscience software for FAIR image segmentation.

Getting started

  1. Click the SPARC VOCABULARY SERVICES button in the TRACE ribbon to open the dialog to gain access to SciCrunch, an anatomical terminology database compliant with FAIR data principles (if you have an internet connection).
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Getting an API Key to Access SciCrunch

To enable this functionality, you need to obtain an API key from SciCrunch that you will use in MBF Bioscience software.

  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 MBF Bioscience software.

  6. Return to the MBF Bioscience application and paste the key in the dialog (right-click and select paste; CTRL-V doesn’t work), then click SET API KEY.

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Accessing Anatomical Terminology

  1. Once you're connected to the SciCrunch database with your API key, select the appropriate items from the drop-downs (see descriptions below).
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Subject information

SPECIES, SUBJECT ID, SEX, and AGE are metadata that will be stored to the XML file. They are independent from the criteria for anatomic terms selected. Note the “blinded to condition” options for sex and age.

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Criteria for anatomic terms

ORGAN: the organ term list you are interested in annotating with.

SPECIES: the species you are interested in annotating with.

PARCELLATION: the atlas parcellation scheme you are interested in annotating with. If you don’t see the parcellation, select Species Independent from the dropdown.

File-level metadata indicating the organ, species, and parcellation selected in the SPARC Vocabulary Services dialog will be stored in the XML with every annotation.

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Annotating Contours

  1. Click BEGIN to display the corresponding anatomical terminology list that you will use for segmentation.

  2. Click the CONTOUR SELECTION button in the TRACE tab to open the Contour Selection Toolbar.

  3. Search for a term.

  4. Select a term and begin contouring regions of interest.

  5. Save data file as XML.

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