Table 1.
3D Microscopy Metadata Standards (3D-MMS) Required Fields.
| Field Name | Definition | Allowable Values | Supports Digital Object Identifier (DOI)? |
|---|---|---|---|
| Contributors Category (nine required metadata fields) | |||
| contributorName | Person (last name, first name) or organization (e.g., research group, department, institution) contributing to or responsible for the project, but does not include funders of the project. If a contributor has more than one contributorType, use a separate line for each. | Free text | Yes |
| Creator | Main researchers involved in producing the data. There must be at least one creator. | Yes; No | Yes |
| contributorType | Categorization of the role of the contributor. Recommended: ProjectLeader (for principal investigator), ResearchGroup (for laboratory, department, or division). | ContactPerson; DataCollector; DataCurator; ProjectLeader; ProjectManager; ProjectMember; RelatedPerson; Researcher; ResearchGroup; Other | Yes |
| nameType | Type of contributorName. | Organizational; Personal | Yes |
| nameIdentifier | Alphanumeric code that uniquely identifies an individual or legal entity, (listed in the contributorName field). Accepted identifiers include GRID*, ISNI*, ORCID*, ROR*, and RRID*. Preferred identifiers are ORCID for personal names and ROR for organizational names. Required for Personal nameType. | Free Text | Yes |
| nameIdentifier Scheme | Identifying scheme used in nameIdentifier. Required for Personal nameType. | GRID*; ISNI*; ORCID*; ROR*; RRID* | Yes |
| affiliation | Organizational or institutional affiliation of the contributor. | Free text | Yes |
| affiliationIdentifier | Unique identifier (ROR preferred) for the organizational or institutional affiliation of the contributor. | Free text | Yes |
| affiliationIdentifierScheme | Identifying scheme used in affiliationIdentifier. | GRID*; ISNI*; ORCID*; ROR*; RRID* | Yes |
| Dataset Category (five required metadata fields) | |||
| Title | Short phrase by which the specific dataset is known (e.g., title of a book). | Free text | Yes |
| Rights | Any rights information for the dataset. May be the name of the license and can include embargo or other use restrictions on data (see https://spdx.org/licenses) | Free text | Yes |
| rightsURI | If using a common license and licensing information is online, provide a link to the license. | Free text | Yes |
| rightsIdentifier | If using a common license, provide the Software Package Data Exchange (SPDX) code for the license (see https://spdx.org/licenses). | Free text | Yes |
| Abstract | Additional descriptive information about the dataset, including a brief description and the context in which it was created (e.g., aim of the experiment, what the dataset is expected to show). This abstract will be used on the DOI landing page and will be the primary description of the dataset; it will ideally be more than 100 words. | Free text | Yes |
| Funders Category (five required metadata fields) | |||
| funderName | The name of the funder. | Free text | Yes |
| fundingReferenceIdentifier | Alphanumeric code that uniquely identifies an individual or legal entity. Preferred identifier is ROR. | Free text (or URL) | Yes |
| fundingReferenceIdentifierType | Identifying scheme used in fundingReferenceIdentifier. | GRID*; ISNI*; ORCID*; ROR*; RRID* | Yes |
| awardNumber | Funding code or project number assigned to the grant. | Free text | Yes |
| awardTitle | Title of the grant award. | Free text | Yes |
| Instrument Category (two required metadata fields) | |||
| MicroscopeType | Type of microscope used to capture the image (e.g., inverted, upright, light sheet, confocal, two photon). | Free text | No |
| MicroscopeManufacturerAndModel | Manufacturer and model of the microscope used. | Free text | No |
| Image Category (eight required metadata fields) | |||
| xAxis | Predominant tissue direction as one moves from the left side of the image to the right side of the image. | Left to right; Right to left; Anterior to posterior; Posterior to anterior; Inferior to superior; Superior to inferior; Oblique | No |
| yAxis | Predominant tissue direction as one moves from the top of the image to the bottom of the image. | Left to right; Right to left; Anterior to posterior; Posterior to anterior; Inferior to superior; Superior to inferior; Oblique | No |
| zAxis | Predominant tissue direction as one follows a given pixel position through the stack of images from the first image to the last image. | Left to right; Right to left; Anterior to posterior; Posterior to anterior; Inferior to superior; Superior to inferior; Oblique | No |
| Number | Number assigned to each channel. | Free text | No |
| displayColor | Original display color for rendering each channel in triplet (red, green, blue) format. | Free text | No |
| stepSizeX | Physical step size in X dimension (e.g., pixel size represents how many microns). | Free text | No |
| stepSizeY | Physical step size in Y dimension (e.g., pixel size represents how many microns). | Free text | No |
| stepSizeZ | Distance between the center of one image and the center of adjacent images in Z dimension (space in microns between slices). | Free text | No |
| Specimen Category (five required metadata fields) | |||
| Species | Common organism classification name for the donor organism (e.g., mouse, human). | Free text | No |
| NCBITaxonomy | National Center for Biotechnology Information (NCBI) taxonomy code for species of the donor organism. | Free text | No |
| Age | Age of the donor (or unknown). | Number | No |
| Ageunit | Unit for the age of the donor. | Days; Months; Years | No |
| Sex | Sex of the donor. | Male; Female; Unknown | No |
*For more information on the identifiers, see the Global Research Identifier Database (GRID, https://www.grid.ac); International Standard Name Identifier (ISNI, https://isni.org); Open Researcher and Contributor ID (ORCID, https://orcid.org); Research Organization Registry (ROR, https://ror.org); and Research Resource Identifiers (RRID, https://scicrunch.org/resources) websites.