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

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)

 

 

Occurrence

0-n = optional and repeatable

0-1 = optional, but not repeatable

1-n = required and repeatable

1 = required, but not repeatable

 

 

 

 

Supplementary Table 2. Instrument Metadata

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

 

 

Occurrence

0-n = optional and repeatable

0-1 = optional, but not repeatable

1-n = required and repeatable

1 = required, but not repeatable

 

 

 

Supplementary Table 3. Image Metadata

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

 

Occurrence

0-n = optional and repeatable

0-1 = optional, but not repeatable

1-n = required and repeatable

1 = required, but not repeatable

 

 

Supplementary Table 4. Specimen Metadata

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

 

Occurrence

0-n = optional and repeatable

0-1 = optional, but not repeatable

1-n = required and repeatable

1 = required, but not repeatable

 

 

 

 

Supplementary Table 5. Publication Metadata

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

 

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).