New Metadata Model
Overview
The BRAIN Image Library (BIL) is transitioning to a new metadata model. Many of the fields that will be required in the near future are shown below. For more information about the model, please see the following preprint:
Essential Metadata for 3D BRAIN Microscopy
Alexander J. Ropelewski, Megan A. Rizzo, Jason R. Swedlow, Jan Huisken, Pavel Osten, Neda Khanjani, Kurt Weiss, Vesselina Bakalov, Michelle Engle, Lauren Gridley, Michelle Krzyzanowski, Tom Madden, Deborah Maiese, Justin Waterfield, David Williams, Carol Hamilton, Wayne Huggins
arXiv:2105.09158v1, 2021 https://arxiv.org/abs/2105.09158
The tables shown below can be downloaded in PDF format from the DORY website.
Supplementary Table 1. Dataset Metadata
Occurrence
0-n = optional and repeatable
0-1 = optional, but not repeatable
1-n = required and repeatable
1 = required, but not repeatable
| Field Name | Definition | Allowable Values | Required | Occurrence | DataCite (ID: Property) | Open Microscopy Environment (Element: Attribute) | |
|---|---|---|---|---|---|---|---|
| Short Descriptions | |||||||
| Title | Short phrase by which the specific dataset is known (e.g., title of a book). | Free text | Yes | 1 | 3: Title | Dataset: Description (can be mapped) | |
| socialMedia | Suggested short social media text describing the dataset to be posted after the dataset is available (can include tags). May be the same as the title. | Free text | No | 0-1 | none | Dataset: Description (can be mapped) | |
| Subject | Description of the dataset using keywords, classification codes, or key phrases. | Free text | No | 0-1 | 6: Subject | none | |
| subjectScheme | Name of the subject scheme or classification (e.g., Allen Mouse Brain Atlas Version2). | Free text | No | 0-1 | none | none | |
| 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 | 1 | 16: Rights | RightsHeld: none (can be mapped) | |
| rightsURI | If using a common license and licensing information is online, provide a link to the license. | Free text | Yes | 1 | 16.a: rightsURI | RightsHeld: none (can be mapped) | |
| 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 | 1 | 16.b: rightsIdentifier | RightsHeld: none (can be mapped) | |
| Image | Suggested static image or animated GIF to associate with the social media and/or web landing page for the dataset. | Free text | No | 0-1 | none | none | |
| generalModality | Description of the general modality of the dataset. | Cell morphology Connectivity Population imaging Spatial transcriptomics Other | No | 0-1 | none | Experiment: Type | |
| generalModalityOther | If generalModality is Other, list the modality used. | Free text | No | 0-1 | none | Experiment: Type | |
| Technique | Description of the technique used. | Anterograde tracing DARTFISH fMOST MERFISH Patch-seq Retrograde Retrograde tracing smFISH Transynaptic tracing TRIO tracing Other | No | 0-1 | Experiment: Type | ||
| techniqueOther | If Technique is Other, list the technique used. | Free text | No | 0-1 | none | Experiment: Type | |
| Detailed Descriptions | |||||||
| 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 Digital Object Identifier (DOI) landing page and will be the primary description of the dataset; it will ideally be 100+ words. | Free text | Yes | 1 | 17: Description 17.a: descriptionType (can be mapped) | Dataset: Description (can be mapped) | |
| Methods | Additional descriptive information about how the biological materials were processed by the laboratories involved. May be used to describe the methodology (or protocols) used. | Free text | No | 0-1 | 17: Description 17.a: descriptionType (can be mapped) | Dataset: Description (can be mapped) | |
| technicalInfo | Additional descriptive information about how the data were processed computationally by the laboratories involved. May be used to describe the computational processing done with software versions and parameters. | Free text | No | 0-1 | 17: Description 17.a: descriptionType (can be mapped) | Dataset: Description (can be mapped) | |
Supplementary Table 2. Instrument Metadata
Occurrence
0-n = optional and repeatable
0-1 = optional, but not repeatable
1-n = required and repeatable
1 = required, but not repeatable
| Field Name | Definition | Allowable Values | Required | Occurrence | DataCite (ID: Property) | Open Microscopy Environment (Element: Attribute) |
|---|---|---|---|---|---|---|
| microscopeType | Type of microscope used to capture the image (e.g., inverted, upright, light sheet, confocal, two photon). | Free text | Yes | 1 | none | Microscope: Type |
| microscopeManufacturerAndModel | Manufacturer and model of the microscope used. | Free text | Yes | 1 | none | Microscope: Manufacturer Microscope: Model |
| objectiveManufacturerAndModel | Manufacturer and model of the lens used. | Free text | No | 1 | none | Objective: Manufacturer Objective: Model |
| objectiveImmersion | Immersion medium for the lens. Suggested values: Air, Glycerol, Multi, Oil, Water, Water dipping. | Free text | No | 1 | none | Objective: Immersion |
| objectiveNA | Lens numerical aperture. | Free text | No | 1 | none | Objective: LensNA |
| objectiveMagnification | Lens magnification. | Free text | No | 1 | none | Objective: NominalMagnification |
| detectorType | Type of detector used. Suggested values: CCD, IntensifiedCCD, AnalogVideo, PMT, Photodiode, CMOS, EBCCD, FTIR, Spectroscopy, LifetimeImaging, CorrelationSpectroscopy, EMCCD, APD. | Free text | No | 1 | none | Detector: Type |
| detectorManufacturerAndModel | Manufacturer and model of the detector. | Free text | No | 1 | none | Detector: Model Detector: Manufacturer |
| illuminationType | Type of illumination. Suggested values: Gas, MetalVapor, SolidState, Dye, Semiconductor, FreeElectron. | Free text | No | 1 | none | Laser: Type |
| illuminationWavelength | Bandwidth of illumination light. | Free text | No | 1 | none | Laser: Wavelength Laser: WavelengthUnit |
| detectionWavelength | Bandwidth of collected light. | Free text | No | 1 | none | none |
| sampleTemperature | Sample temperature at capture. | Free text | No | 1 | none | ImagingEnvironment: Temperature ImagingEnvironment: TemperatureUnit |
Supplementary Table 3. Image Metadata
Occurrence
0-n = optional and repeatable
0-1 = optional, but not repeatable
1-n = required and repeatable
1 = required, but not repeatable
| Field Name | Definition | Allowable Values | Required | Occurrence | DataCite (ID: Property) | Open Microscopy Environment (Element: Attribute) | |
|---|---|---|---|---|---|---|---|
| Orientation | |||||||
| 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 |
Yes | 1 | none | StageLabel: X StageLabel: XUnit | |
| obliqueXDim1 | Only if xAxis is oblique, enter the orientation. | Left Right | Required if xAxis is oblique | 1 | none | none | |
| obliqueXDim2 | Only if xAxis is oblique, enter the orientation. | Anterior Posterior | Required if xAxis is oblique | 1 | none | none | |
| obliqueXDim3 | Only if xAxis is oblique, enter the orientation. | Inferior Superior | Required if xAxis is oblique | 1 | none | none | |
| 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 |
Yes | 1 | none | StageLabel: Y StageLabel: YUnit | |
| obliqueYDim1 | Only if yAxis is oblique, enter the orientation. | Left Right | Required if yAxis is oblique | 1 | none | none | |
| obliqueYDim2 | Only if yAxis is oblique, enter the orientation. | Anterior Posterior | Required if yAxis is oblique | 1 | none | none | |
| obliqueYDim3 | Only if yAxis is oblique, enter the orientation. | Inferior Superior | Required if yAxis is oblique | 1 | none | none | |
| 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 |
Yes | 1 | none | StageLabel: Z StageLabel: ZUnit | |
| obliqueZDim1 | Only if zAxis is oblique, enter the orientation. | Left Right | Required if zAxis is oblique | 1 | none | none | |
| obliqueZDim2 | Only if zAxis is oblique, enter the orientation. | Anterior Posterior | Required if zAxis is oblique | 1 | none | none | |
| obliqueZDim3 | Only if zAxis is oblique, enter the orientation. | Inferior Superior | Required if zAxis is oblique | 1 | none | none | |
| Landmark | |||||||
| landmarkName | Name of the landmark (e.g., bregma). | Free text | No | 0-1 | none | none | |
| landmarkX | X coordinate of the landmark. | Free text | No | 0-1 | none | none | |
| landmarkY | Y coordinate of the landmark. | Free text | No | 0-1 | none | none | |
| landmarkZ | Z coordinate of the landmark. | Free text | No | 0-1 | none | none | |
| Channel | |||||||
| Number | Number assigned to each channel. | Free text | Yes | 1 | none | Channel: ChannelID | |
| displayColor | Display color of each channel in triplet (red, green, blue) format. | Free text | Yes | 1-n | none | Channel: Color | |
| Representation | What the channel represents (e.g., rhodopsin, virus). | Free text | No | 0-1 | none | Channel: Name | |
| Size | |||||||
| Flurophore | Fluorophore used in the channel (e.g., egfp, alexa-561, ATO-647). | none | Channel: Fluor | ||||
| stepSizeX | Physical step size in the X-dimension (e.g., pixel size represents the number of microns). | Free text | Yes | 1 | none | Pixels: PhysicalSizeX Pixels: PhysicalSizeXUnit | |
| stepSizeY | Physical step size in the Y-dimension (e.g., pixel size represents the number of microns). | Free text | Yes | 1 | none | Pixels: PhysicalSizeY Pixels: PhysicalSizeYUnit | |
| stepSizeZ | Distance between the center of one image and the center of adjacent images in the Z-dimension (space in microns between slices). | Free text | No | 0-1 | none | Pixels: PhysicalSizeZ Pixels: PhysicalSizeZUnit | |
| stepSizeT | Physical step size in the T dimension (time). | Free text | No | 0-1 | none | Pixels: TimeIncrement Pixels: TimeIncrementUnit | |
| Channel | Number of channels. | Free text | No | 0-1 | none | ||
| Slice | Number of slices per channel (approximate). | Free text | No | 0-1 | none | ||
| z | Number of timepoints. | Free text | No | 0-1 | none | ||
| xSize | Number of pixels in the X-dimension. | Free text | No | 0-1 | none | Pixels: SizeX | |
| ySize | Number of pixels in the Y-dimension. | Free text | No | 0-1 | none | Pixels: SizeY | |
| zSize | Number of pixels in the Z-dimension. | Free text | No | 0-1 | none | Pixels: SizeZ | |
| Gbyte | Total size in gigabytes. | Free text | No | 0-1 | none | ||
| File | Total number of image files. | Free text | No | 0-1 | none | ||
| dimensionOrder | XYZT, or whatever order is used. | Free text | No | 0-1 | none | Pixels: DimensionOrder | |
Supplementary Table 4. Specimen Metadata
Occurrence
0-n = optional and repeatable
0-1 = optional, but not repeatable
1-n = required and repeatable
1 = required, but not repeatable
| Field Name | Definition | Allowable Values | Required | Occurrence | DataCite (ID: Property) | Open Microscopy Environment (Element: Attribute) |
|---|---|---|---|---|---|---|
| Donor | ||||||
| localID | Local (lab) reference ID attached to the donor organism (if any). | Free text | No | 0-1 | none | none |
| Species | Common organism classification name for the donor organism (e.g., mouse, human). | Free text | Yes | 1 | none | none |
| NCBITaxonomy | National Center for Biotechnology Information (NCBI) taxonomy code for species of the donor organism. | Free text | Yes | 1 | none | none |
| Age | Age of the donor (or unknown). | Free text | Yes | 1 | none | none |
| ageUnit | Unit for the age of the donor. | Days Months Years | Yes | 1 | none | none |
| Sex | Sex of the donor. | Female Male Unknown | Yes | 1 | none | none |
| Genotype | If relevant, genotype or transgenetic line information (e.g., Strain name, Cre driver line, Reporter name). | Free text | No | 0-1 | none | none |
| Organ | ||||||
| organLocalID | Local (lab) reference ID attached to the organ (if any). | Free text | No | 0-1 | none | none |
| organName | Component part of the nervous system where the tissue is found (e.g., brain, spinal cord). | Free text | No | 0-1 | none | none |
| Sample | ||||||
| sampleLocalID | Local (lab) reference ID attached to the sample (if any). | Free text | No | 0-1 | none | none |
| Atlas | If an atlas was used to describe the location, list the name of the atlas. Suggested values: Allen Mouse V1, Allen Mouse V2, Allen Mouse V3, Allen Human 34yrs Whole Brain, Whole Brain. | Free text | No | 0-1 | none | none |
| Location | (Sub)location or region where the tissue is found. | Free text | No | 0-1 | none | none |
Supplementary Table 5. Publication Metadata
Occurrence
0-n = optional and repeatable
0-1 = optional, but not repeatable
1-n = required and repeatable
1 = required, but not repeatable
* For more information on the identifier schemes, see the arXiv
distribution service (https://arxiv.org), the
international digital object identifier (DOI) foundation (https://www.doi.org), the US International Standard
Book Number (ISBN) Agency (http://www.isbn.org),
and the PubMed Identifiers (PMID) on the PubMed website (https://pubmed.ncbi.nlm.nih.gov).
| Field Name | Definition | Allowable Values | Required | Occurrence | DataCite (ID: Property) | Open Microscopy Environment (Element: Attribute) |
|---|---|---|---|---|---|---|
| relatedIdentifier | Alphanumeric code that uniquely identifies the publication or other related information. | Free text | No | 0-n | 12: relatedIdentifier | None |
| relatedIdentifierType | Identifying scheme used in relatedIdentifier. Recommended: DOI, PMID. | arXiv* DOI* ISBN* PMID* | No | 0-n | 12.a: relatedIdentifierType | None |
| PMCID | PubMed Central identifier (PMCID; if applicable). | Free text | No | 0-n | None | None |
| relationType | DataCite descriptive identifier specifying the relationship. | IsCitedBy IsDocumentedBy | No | 0-n | 12.b: relationType | None |
| Citation | Complete citation for the publication or other related information. | Free text | No | 0-n | None | None |