What the data looks like in the database after processing

Cell Feature Database Specification

Structure of the data stored in firebase and AWS

Table 1. `Cell Feature Database Specification` Properties
	Type	Description	Required
dataset-descriptions	`dataset-descriptions`	Endpoint that gets called first to load all the available datasets. Each DATASET_ID maps to a megaset card	✓ Yes
manifests	`object`	Collection of manifests for each published dataset.	✓ Yes
dataset-data	`object`	High level data for a dataset, ie not per cell data	✓ Yes
cell-data	`object`	Per cell data	✓ Yes
measured-features	`array-items/condensed-measured-feature` `[]`	File stored on AWS that has the condensed measured data. Is an array of condensed measured features.	✓ Yes

Additional properties are not allowed.

JSON schema: database.schema.json

Cell Feature Database Specification.dataset-descriptions

Endpoint that gets called first to load all the available datasets. Each DATASET_ID maps to a megaset card

Type: dataset-descriptions
Required: ✓ Yes

Cell Feature Database Specification.manifests

Collection of manifests for each published dataset.

Type: object
Required: ✓ Yes

Cell Feature Database Specification.dataset-data

High level data for a dataset, ie not per cell data

Type: object
Required: ✓ Yes

Cell Feature Database Specification.cell-data

Per cell data

Type: object
Required: ✓ Yes

Cell Feature Database Specification.measured-features

File stored on AWS that has the condensed measured data. Is an array of condensed measured features.

Type: array-items/condensed-measured-feature []
Required: ✓ Yes

Condensed measured feature

Data per cell needed to create the CFE plot

Table 2. `Condensed measured feature` Properties
	Type	Description	Required
f	`(number or string)[]`	ordered array of measured features	✓ Yes
p	`string`	Protein name	✓ Yes
t	`string`	Thumbnail Path	✓ Yes
i	`string`	Cell id	✓ Yes

Additional properties are not allowed.

JSON schema: array-items/condensed-measured-feature.schema.json

array-items/condensed-measured-feature.f

ordered array of measured features

Type: (number or string)[]
- Each element in the array must be one of the following values:
Required: ✓ Yes

array-items/condensed-measured-feature.p

Protein name

Type: string
Required: ✓ Yes

array-items/condensed-measured-feature.t

Thumbnail Path

Type: string
Required: ✓ Yes

array-items/condensed-measured-feature.i

Cell id

Type: string
Required: ✓ Yes

Condensed measured features JSON

File stored on AWS that has the condensed measured data. Is an array of condensed measured features.

Type: array-items/condensed-measured-feature
JSON schema: measured-features.schema.json

Dataset Card

Data needed to render a dataset card

Table 3. `Dataset Card` Properties
	Type	Description	Required
title	`string`	Display name of dataset.	✓ Yes
name	`string`	Name of the group (no version number). Lowercase with underscores.	✓ Yes
version	`string`	Version year and number	✓ Yes
description	`string`	Description of the dataset	✓ Yes
extra	`string`	Extra text to display on the card with a callout box	No
image	`string`	Url of the dataset card image file on AWS	No
link	`string`	Link to website displaying the dataset	No
userData	`userData`	Optional display data	No
production	`boolean`	Whether this dataset should be shown in production	No
index	`number`	Index of dataset in a megaset.	No
datasetLinks	`array-items/dataset-link` `[]`	Array of dataset links	No

Additional properties are not allowed.

JSON schema: dataset-card.schema.json

dataset-card.title

Display name of dataset.

Type: string
Required: ✓ Yes

dataset-card.name

Name of the group (no version number). Lowercase with underscores.

Type: string
Required: ✓ Yes

dataset-card.version

Version year and number

Type: string
Required: ✓ Yes

dataset-card.description

Description of the dataset

Type: string
Required: ✓ Yes

dataset-card.extra

Extra text to display on the card with a callout box

Type: string
Required: No

dataset-card.image

Url of the dataset card image file on AWS

Type: string
Required: No

dataset-card.link

Link to website displaying the dataset

Type: string
Required: No

dataset-card.userData

Optional display data

Type: userData
Required: No

dataset-card.production

Whether this dataset should be shown in production

Type: boolean
Required: No

dataset-card.index

Index of dataset in a megaset.

Type: number
Required: No

dataset-card.datasetLinks

Array of dataset links

Type: array-items/dataset-link []
Required: No

Dataset Description Collection

Endpoint that gets called first to load all the available datasets. Each DATASET_ID maps to a megaset card

Mapping interface: { [ key: ^(\w{1,})_(v\d{4}.\d{1,}|\w{1,})$ ]: megaset-card }

Table 4. `megaset-card` Properties
	Type	Description	Required
datasets	`dataset-card` `[]`	Array of dateset cards.	✓ Yes
dateCreated	`string`	Format: Firebase Timestamp.	✓ Yes
name	`string`	Name of the group (no version number). Lowercase with underscores.	✓ Yes
production	`boolean`	Whether this dataset should be shown in production	✓ Yes
title	`string`	Display name of dataset group.	✓ Yes
publications	`publication` `[]`	Publications associated with the group	No

Additional properties are allowed.

JSON schema: dataset-descriptions.schema.json

Dataset Link

Schema for each single dataset

Table 5. `Dataset Link` Properties
	Type	Description	Required
date	`string`	Date of the dataset release	✓ Yes
title	`string`		✓ Yes
link	`string`		✓ Yes

Additional properties are not allowed.

JSON schema: array-items/dataset-link.schema.json

array-items/dataset-link.date

Date of the dataset release

Type: string
Required: ✓ Yes

array-items/dataset-link.title

Type: string
Required: ✓ Yes

array-items/dataset-link.link

Type: string
Required: ✓ Yes

Discrete feature option

Schema for each category in a discrete feature

Table 6. `Discrete feature option` Properties
	Type	Description	Required
color	`string`	Hex string	✓ Yes
name	`string`	Display name for the option. Doesn’t have to be unique, but if it’s not unique, `key` is required.	✓ Yes
key	`string`	unique key for the option.	No

Additional properties are not allowed.

JSON schema: array-items/discrete-feature-option.schema.json

array-items/discrete-feature-option.color

Hex string

Type: string
Required: ✓ Yes

array-items/discrete-feature-option.name

Display name for the option. Doesn’t have to be unique, but if it’s not unique, key is required.

Type: string
Required: ✓ Yes

array-items/discrete-feature-option.key

unique key for the option.

Type: string
Required: No

Discrete feature options

Mapping of numeral key in the analysis to category names. There should be one key value pair for each category of a discrete feature. For example, if the feature is a boolean, and the numeral data is either 0 or 1, there should be two option mappings.

Mapping interface: { [ key: ^\d{1,}$ ]: array-items/discrete-feature-option }

Table 7. `array-items/discrete-feature-option` Properties
	Type	Description	Required
color	`string`	Hex string	✓ Yes
name	`string`	Display name for the option. Doesn’t have to be unique, but if it’s not unique, `key` is required.	✓ Yes
key	`string`	unique key for the option.	No

Additional properties are allowed.

JSON schema: discrete-feature-options.schema.json

Feature data order

Ordered array of feature keys for packing and unpacking data

Type: string
JSON schema: definitions.schema.json

Feature Definition

Definition of a measured features in the dataset. Feature definitions file is an array of these objects.

Table 8. `Feature Definition` Properties
	Type	Description	Required
displayName	`string`	Human readable name	✓ Yes
description	`string`	Description of how the data was collected/measured	No
tooltip	`string`	Shorter version of description	No
unit	`string`	unit of measurement	✓ Yes
key	`string`	Id of the feature	✓ Yes
discrete	`boolean`	Whether it’s a continuous measurement or not	✓ Yes
options	`discrete-feature-options`	Mapping of numeral key in the analysis to category names. There should be one key value pair for each category of a discrete feature. For example, if the feature is a boolean, and the numeral data is either `0` or `1`, there should be two option mappings.	No

Additional properties are not allowed.

JSON schema: feature-def.schema.json

feature-def.displayName

Human readable name

Type: string
Required: ✓ Yes

feature-def.description

Description of how the data was collected/measured

Type: string
Required: No

Shorter version of description

Type: string
Required: No

feature-def.unit

unit of measurement

Type: string
Required: ✓ Yes

feature-def.key

Id of the feature

Type: string
Required: ✓ Yes

feature-def.discrete

Whether it’s a continuous measurement or not

Type: boolean
Required: ✓ Yes

feature-def.options

Type: discrete-feature-options
Required: No

Feature display order

Ordered array of feature keys for display on front end

Type: string
JSON schema: definitions.schema.json

File info

File info for one cell, this is the data needed to access images for the cell.

Table 9. `File info` Properties
	Type	Description	Required
CellId	`string`	unique id for segmented cell	✓ Yes
FOVId	`string`	Field of view cell came from	✓ Yes
groupBy	`string`	Id of feature the data is grouped by by default	✓ Yes
thumbnailPath	`string`	Path to thumbnail image for cell	No
volumeviewerPath	`string`	path to 3d data for cell	✓ Yes
fovThumbnailPath	`string`	Path to fov thumbnail	No
fovVolumeviewerPath	`string`	Path to the fov 3d data	No
transform	`object`	Transform to apply to the cell	No

Additional properties are not allowed.

JSON schema: array-items/file-info.schema.json

array-items/file-info.CellId

unique id for segmented cell

Type: string
Required: ✓ Yes

array-items/file-info.FOVId

Field of view cell came from

Type: string
Required: ✓ Yes

array-items/file-info.groupBy

Id of feature the data is grouped by by default

Type: string
Required: ✓ Yes

array-items/file-info.thumbnailPath

Path to thumbnail image for cell

Type: string
Required: No

array-items/file-info.volumeviewerPath

path to 3d data for cell

Type: string
Required: ✓ Yes

array-items/file-info.fovThumbnailPath

Path to fov thumbnail

Type: string
Required: No

array-items/file-info.fovVolumeviewerPath

Path to the fov 3d data

Type: string
Required: No

array-items/file-info.transform

Transform to apply to the cell

Type: object
Required: No

Input datasets

Array of dateset cards.

Type: dataset-card
JSON schema: definitions.schema.json

Manifest

High level data for each dataset that points to where all the data is stored for this dataset.

Table 10. `Manifest` Properties
	Type	Description	Required
featuresDataPath	`string`	Url of the features JSON on AWS	✓ Yes
featureDefsPath	`string`	Database path to feature definition collection	No
viewerSettingsPath	`string`	Url of the per-channel settings file for the 3d viewer on AWS.	✓ Yes
albumPath	`string`	Database path to album information.	✓ Yes
thumbnailRoot	`string`	Root url for thumbnail images	✓ Yes
downloadRoot	`string`	Root url for downloading cell data	✓ Yes
volumeViewerDataRoot	`string`	Root url for 3d images	✓ Yes
xAxis	`selection-settings`		✓ Yes
yAxis	`selection-settings`		✓ Yes
colorBy	`selection-settings`		✓ Yes
groupBy	`selection-settings`		✓ Yes
featuresDisplayOrder	`string` `[]`	Ordered array of feature keys for display on front end	✓ Yes
featuresDataOrder	`string` `[]`	Ordered array of feature keys for packing and unpacking data	✓ Yes

Additional properties are not allowed.

JSON schema: manifest.schema.json

manifest.featuresDataPath

Url of the features JSON on AWS

Type: string
Required: ✓ Yes

manifest.featureDefsPath

Database path to feature definition collection

Type: string
Required: No

manifest.viewerSettingsPath

Url of the per-channel settings file for the 3d viewer on AWS.

Type: string
Required: ✓ Yes

manifest.albumPath

Database path to album information.

Type: string
Required: ✓ Yes

manifest.thumbnailRoot

Root url for thumbnail images

Type: string
Required: ✓ Yes

manifest.downloadRoot

Root url for downloading cell data

Type: string
Required: ✓ Yes

manifest.volumeViewerDataRoot

Root url for 3d images

Type: string
Required: ✓ Yes

manifest.xAxis

Type: selection-settings
Required: ✓ Yes

manifest.yAxis

Type: selection-settings
Required: ✓ Yes

manifest.colorBy

Type: selection-settings
Required: ✓ Yes

manifest.groupBy

Type: selection-settings
Required: ✓ Yes

manifest.featuresDisplayOrder

Ordered array of feature keys for display on front end

Type: string []
Required: ✓ Yes

manifest.featuresDataOrder

Ordered array of feature keys for packing and unpacking data

Type: string []
Required: ✓ Yes

Megaset Card

Data needed to render a megaset card

Table 11. `Megaset Card` Properties
	Type	Description	Required
datasets	`dataset-card` `[]`	Array of dateset cards.	✓ Yes
dateCreated	`string`	Format: Firebase Timestamp.	✓ Yes
name	`string`	Name of the group (no version number). Lowercase with underscores.	✓ Yes
production	`boolean`	Whether this dataset should be shown in production	✓ Yes
title	`string`	Display name of dataset group.	✓ Yes
publications	`publication` `[]`	Publications associated with the group	No

Additional properties are not allowed.

JSON schema: megaset-card.schema.json

megaset-card.datasets

Array of dateset cards.

Type: dataset-card []
Required: ✓ Yes

megaset-card.dateCreated

Format: Firebase Timestamp.

Type: string
Required: ✓ Yes

megaset-card.name

Name of the group (no version number). Lowercase with underscores.

Type: string
Required: ✓ Yes

megaset-card.production

Whether this dataset should be shown in production

Type: boolean
Required: ✓ Yes

megaset-card.title

Display name of dataset group.

Type: string
Required: ✓ Yes

megaset-card.publications

Publications associated with the group

Type: publication []
Required: No

Publication

Publication data

Table 12. `Publication` Properties
	Type	Description	Required
title	`string`	Article title	No
url	`string`	Article link	No
citation	`string`	Article journal and date	No

Additional properties are not allowed.

JSON schema: definitions.schema.json

publication.title

Article title

Type: string
Required: No

publication.url

Article link

Type: string
Required: No

publication.citation

Article journal and date

Type: string
Required: No

Selection settings

Table 13. `Selection settings` Properties
	Type	Description	Required
default	`string`	Default feature key for the setting	✓ Yes
exclude	`string` `[]`	Optional list of feature keys to exclude	No

Additional properties are not allowed.

JSON schema: definitions.schema.json

selection-settings.default

Default feature key for the setting

Type: string
Required: ✓ Yes

selection-settings.exclude

Optional list of feature keys to exclude

Type: string []
Required: No

User data

Optional display data

Additional properties are allowed.

JSON schema: definitions.schema.json

Appendix

JSON Schema for Cell Feature Database Specification

{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "$id": "database-schema",
    "title": "Cell Feature Database Specification",
    "description": "Structure of the data stored in firebase and AWS",
    "type": "object",
    "additionalProperties": false,
    "properties": {
        "dataset-descriptions": {
            "$ref": "dataset-descriptions.schema.json"
        },
        "manifests": {
            "description": "Collection of manifests for each published dataset.",
            "type": "object",
            "patternProperties": {
                "^(\\w{1,})_(v\\d{4}.\\d{1,}|\\w{1,})$": {
                    "type": "object",
                    "$ref": "manifest.schema.json"
                }
            }
        },
        "dataset-data": {
            "$id": "dataset-data",
            "description": "High level data for a dataset, ie not per cell data",
            "type": "object",
            "properties": {
                "feature-definitions": {
                    "type": "object",
                    "patternProperties": {
                        "^(\\w{1,})_(v\\d{4}.\\d{1,}|\\w{1,})$": {
                            "type": "object",
                            "$feature-key": {
                                "$ref": "feature-def.schema.json"
                            }
                        }
                    }
                }
            }
        },
        "cell-data": {
            "description": "Per cell data",
            "$id": "cell-data",
            "type": "object",
            "patternProperties": {
                "^(\\w{1,})_(v\\d{4}.\\d{1,}|\\w{1,})$": {
                    "type": "object",
                    "properties": {
                        "cell-file-info": {
                            "type": "object",
                            "description": "Per cell mapping of file info",
                            "patternProperties": {
                                "^\\d{1,}$": {
                                    "$ref": "array-items/file-info.schema.json"
                                }
                            }
                        }
                    }
                }
            }
        },
        "measured-features": {
            "$ref": "measured-features.schema.json"
        }
    },
    "required": [
        "dataset-descriptions",
        "manifests",
        "dataset-data",
        "cell-data",
        "measured-features"
    ]
}

JSON Schema for Condensed measured feature

{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "$id": "array-items/condensed-measured-feature.schema.json",
    "title": "Condensed measured feature",
    "description": "Data per cell needed to create the CFE plot",
    "additionalProperties": false,
    "type": "object",
    "properties": {
        "f": {
            "description": "ordered array of measured features",
            "type": "array",
            "items": {
                "anyOf": [
                    {
                        "type": "number"
                    },
                    {
                        "type": "string",
                        "pattern": "[NaN]"
                    }
                ]
            }
        },
        "p": {
            "description": "Protein name",
            "type": "string"
        },
        "t": {
            "description": "Thumbnail Path",
            "type": "string"
        },
        "i": {
            "description": "Cell id",
            "type": "string"
        }
    },
    "required": [
        "f",
        "p",
        "t",
        "i"
    ]
}

JSON Schema for Condensed measured features JSON

{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "$id": "measured-features.schema.json",
    "title": "Condensed measured features JSON",
    "description": "File stored on AWS that has the condensed measured data. Is an array of condensed measured features.",
    "type": "array",
    "items": {
        "$ref": "array-items/condensed-measured-feature.schema.json"
    }
}

JSON Schema for Dataset Card

{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "$id": "dataset-card.schema.json",
    "title": "Dataset Card",
    "description": "Data needed to render a dataset card",
    "type": "object",
    "additionalProperties": false,
    "properties": {
        "title": {
            "$ref": "definitions.schema.json#/definitions/dataset-title"
        },
        "name": {
            "$ref": "definitions.schema.json#/definitions/name"
        },
        "version": {
            "$ref": "definitions.schema.json#/definitions/version"
        },
        "description": {
            "$ref": "definitions.schema.json#/definitions/description"
        },
        "extra": {
            "$ref": "definitions.schema.json#/definitions/extra"
        },
        "image": {
            "$ref": "definitions.schema.json#/definitions/processed-image"
        },
        "link": {
            "$ref": "definitions.schema.json#/definitions/link"
        },
        "userData": {
            "$ref": "definitions.schema.json#/definitions/userData"
        },
        "production": {
            "$ref": "definitions.schema.json#/definitions/production"
        },
        "index": {
            "$ref": "definitions.schema.json#/definitions/index"
        },
        "datasetLinks": {
            "$ref": "definitions.schema.json#/definitions/datasetLinks"
        }
    },
    "required": [
        "title",
        "version",
        "name",
        "description"
    ]
}

JSON Schema for Dataset Description Collection

{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "$id": "dataset-descriptions",
    "title": "Dataset Description Collection",
    "description": "Endpoint that gets called first to load all the available datasets. Each DATASET_ID maps to a megaset card",
    "type": "object",
    "patternProperties": {
        "^(\\w{1,})_(v\\d{4}.\\d{1,}|\\w{1,})$": {
            "$ref": "megaset-card.schema.json"
        }
    }
}

JSON Schema for Dataset Link

{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "$id": "array-items/dataset-link.schema.json",
    "title": "Dataset Link",
    "description": "Schema for each single dataset",
    "additionalProperties": false,
    "type": "object",
    "properties": {
        "date": {
            "description": "Date of the dataset release",
            "type": "string"
        },
        "title":{ 
            "type": "string" 
        },
        "link": { 
            "type": "string" 
        }
    },
    "required": [
        "date",
        "title",
        "link"
    ]
}

JSON Schema for Discrete feature option

{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "$id": "array-items/discrete-feature-option.schema.json",
    "title": "Discrete feature option",
    "description": "Schema for each category in a discrete feature",
    "type": "object",
    "properties": {
        "color": {
            "description": "Hex string",
            "type": "string"
        },
        "name": {
            "description": "Display name for the option. Doesn't have to be unique, but if it's not unique, `key` is required.",
            "type": "string"
        },
        "key": {
            "description": "unique key for the option.",
            "type": "string"
        }
    },
    "additionalProperties": false,
    "required": [
        "name",
        "color"
    ]
}

JSON Schema for Discrete feature options

{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "$id": "discrete-feature-options.schema.json",
    "title": "Discrete feature options",
    "description": "Mapping of numeral key in the analysis to category names. There should be one key value pair for each category of a discrete feature. For example, if the feature is a boolean, and the numeral data is either `0` or `1`, there should be two option mappings.",
    "type": "object",
    "patternProperties": {
        "^\\d{1,}$": {
            "$ref": "array-items/discrete-feature-option.schema.json"
        }
    }
}

JSON Schema for Feature data order

{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "$id": "definitions.schema.json",
    "title": "Definitions of dataset properties",
    "type": "object",
    "additionalProperties": false,
    "definitions": {
        "group-title": {
            "title": "Group title",
            "description": "Display name of dataset group.",
            "type": "string"
        },
        "dataset-title": {
            "title": "Dataset title",
            "description": "Display name of dataset.",
            "type": "string"
        },
        "name": {
            "title": "Dataset name",
            "description": "Name of the group (no version number). Lowercase with underscores.",
            "type": "string"
        },
        "index": {
            "title": "Dataset index",
            "description": "Index of dataset in a megaset.",
            "type": "number"
        },
        "publication": {
            "title": "Publication",
            "description": "Publication data",
            "additionalProperties": false,
            "type": "object",
            "properties": {
                "title": {
                    "description": "Article title",
                    "type": "string"
                },
                "url": {
                    "description": "Article link",
                    "type": "string"
                },
                "citation": {
                    "description": "Article journal and date",
                    "type": "string"
                }
            }
        },
        "version": {
            "title": "Version",
            "description": "Version year and number",
            "type": "string"
        },
        "description": {
            "title": "Description",
            "description": "Description of the dataset",
            "type": "string"
        },
        "extra": {
            "title": "Extra",
            "description": "Extra text to display on the card with a callout box",
            "type": "string"
        },
        "link": {
            "title": "Link (deprecated)",
            "description": "Link to website displaying the dataset",
            "type": "string"
        },
        "userData": {
            "title": "User data",
            "description": "Optional display data",
            "type": "object"
        },
        "production": {
            "title": "Is production",
            "description": "Whether this dataset should be shown in production",
            "type": "boolean"
        },
        "thumbnailRoot": {
            "title": "Thumbnail root",
            "description": "Root url for thumbnail images",
            "type": "string"
        },
        "downloadRoot": {
            "title": "Download root",
            "description": "Root url for downloading cell data",
            "type": "string"
        },
        "volumeViewerDataRoot": {
            "title": "VolumeViewer data root",
            "description": "Root url for 3d images",
            "type": "string"
        },
        "selection-settings": {
            "title": "Selection settings",
            "type": "object",
            "properties": {
                "default": {
                    "description": "Default feature key for the setting",
                    "type": "string"
                },
                "exclude": {
                    "description": "Optional list of feature keys to exclude",
                    "type": "array",
                    "items": {
                        "type": "string"
                    }
                }
            },
            "required": [
                "default"
            ],
            "additionalProperties": false
        },
        "featuresDisplayOrder": {
            "title": "Feature display order",
            "description": "Ordered array of feature keys for display on front end",
            "type": "array",
            "items": {
                "type": "string"
            }
        },
        "featuresDataOrder": {
            "title": "Feature data order",
            "description": "Ordered array of feature keys for packing and unpacking data",
            "type": "array",
            "items": {
                "type": "string"
            }
        },
        "input-dateCreated": {
            "title": "Date the dataset was created",
            "description": "Format: Month Day, Year. If it's not specified, the date will be set to the upload date. ",
            "type": "string"
        },
        "input-datasets": {
            "title": "Input datasets",
            "description": "Array of subfolder names that point to each dataset in the group. Each subfolder should contain their own `dataset.json`.",
            "type": "array",
            "items": {
                "type": "string"
            }
        },
        "input-image": {
            "title": "Image file",
            "description": "Relative path to the dataset card image file, including filename.",
            "type": "string"
        },
        "input-featuresDataPath": {
            "title": "Feature data path",
            "description": "Relative path to the per cell data json, including filename.",
            "type": "string"
        },
        "input-featureDefsPath": {
            "title": "Feature defs path",
            "description": "Relative path to the feature definition file, including filename.",
            "type": "string"
        },
        "input-viewerSettingsPath": {
            "title": "Viewer settings path",
            "description": "Relative path to image per-channel settings file for the 3d viewer, including filename.",
            "type": "string"
        },
        "input-albumPath": {
            "title": "Album path",
            "description": "Relative path to the album file.",
            "type": "string"
        },
        "processed-dateCreated": {
            "title": "Date the dataset was created",
            "description": "Format: Firebase Timestamp. ",
            "type": "string"
        },
        "processed-datasets": {
            "title": "Input datasets",
            "description": "Array of dateset cards.",
            "type": "array",
            "items": {
                "type": "object",
                "$ref": "dataset-card.schema.json"
            }
        },
        "processed-image": {
            "title": "Image file",
            "description": "Url of the dataset card image file on AWS",
            "type": "string"
        },
        "processed-featuresDataPath": {
            "title": "Feature data path",
            "description": "Url of the features JSON on AWS",
            "type": "string"
        },
        "processed-featureDefsPath": {
            "title": "Feature defs path",
            "description": "Database path to feature definition collection",
            "type": "string"
        },
        "processed-viewerSettingsPath": {
            "title": "Viewer settings path",
            "description": "Url of the per-channel settings file for the 3d viewer on AWS.",
            "type": "string"
        },
        "processed-albumPath": {
            "title": "Album path",
            "description": "Database path to album information.",
            "type": "string"
        },
        "datasetLinks": {
            "title": "Dataset Link",
            "description": "Array of dataset links",
            "type": "array",
            "items": {
                "$ref": "array-items/dataset-link.schema.json",
                "type": "object"
            }
        }
    }
}

JSON Schema for Feature Definition

{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "$id": "feature-def.schema.json",
    "title": "Feature Definition",
    "description": "Definition of a measured features in the dataset. Feature definitions file is an array of these objects.",
    "type": "object",
    "additionalProperties": false,
    "properties": {
        "displayName": {
            "description": "Human readable name",
            "type": "string"
        },
        "description": {
            "description": "Description of how the data was collected/measured",
            "type": "string"
        },
        "tooltip": {
            "description": "Shorter version of description",
            "type": "string"
        },
        "unit": {
            "description": "unit of measurement",
            "type": "string"
        },
        "key": {
            "description": "Id of the feature",
            "type": "string"
        },
        "discrete": {
            "description": "Whether it's a continuous measurement or not",
            "type": "boolean"
        },
        "options": {
            "description": "Required for discrete features, options is a mapping of the numeral value in the 'measured' feature to the name and color for that category.",
            "type": "object",
            "$ref": "discrete-feature-options.schema.json"
        }
    },
    "required": [
        "displayName",
        "unit",
        "key",
        "discrete"
    ],
    "allOf": [
        {
            "if": {
                "properties": {
                    "discrete": {
                        "const": true
                    }
                }
            },
            "then": {
                "required": [
                    "options"
                ]
            },
            "else": {
                "not": {
                    "required": [
                        "options"
                    ]
                }
            }
        }
    ]
}

JSON Schema for Feature display order

{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "$id": "definitions.schema.json",
    "title": "Definitions of dataset properties",
    "type": "object",
    "additionalProperties": false,
    "definitions": {
        "group-title": {
            "title": "Group title",
            "description": "Display name of dataset group.",
            "type": "string"
        },
        "dataset-title": {
            "title": "Dataset title",
            "description": "Display name of dataset.",
            "type": "string"
        },
        "name": {
            "title": "Dataset name",
            "description": "Name of the group (no version number). Lowercase with underscores.",
            "type": "string"
        },
        "index": {
            "title": "Dataset index",
            "description": "Index of dataset in a megaset.",
            "type": "number"
        },
        "publication": {
            "title": "Publication",
            "description": "Publication data",
            "additionalProperties": false,
            "type": "object",
            "properties": {
                "title": {
                    "description": "Article title",
                    "type": "string"
                },
                "url": {
                    "description": "Article link",
                    "type": "string"
                },
                "citation": {
                    "description": "Article journal and date",
                    "type": "string"
                }
            }
        },
        "version": {
            "title": "Version",
            "description": "Version year and number",
            "type": "string"
        },
        "description": {
            "title": "Description",
            "description": "Description of the dataset",
            "type": "string"
        },
        "extra": {
            "title": "Extra",
            "description": "Extra text to display on the card with a callout box",
            "type": "string"
        },
        "link": {
            "title": "Link (deprecated)",
            "description": "Link to website displaying the dataset",
            "type": "string"
        },
        "userData": {
            "title": "User data",
            "description": "Optional display data",
            "type": "object"
        },
        "production": {
            "title": "Is production",
            "description": "Whether this dataset should be shown in production",
            "type": "boolean"
        },
        "thumbnailRoot": {
            "title": "Thumbnail root",
            "description": "Root url for thumbnail images",
            "type": "string"
        },
        "downloadRoot": {
            "title": "Download root",
            "description": "Root url for downloading cell data",
            "type": "string"
        },
        "volumeViewerDataRoot": {
            "title": "VolumeViewer data root",
            "description": "Root url for 3d images",
            "type": "string"
        },
        "selection-settings": {
            "title": "Selection settings",
            "type": "object",
            "properties": {
                "default": {
                    "description": "Default feature key for the setting",
                    "type": "string"
                },
                "exclude": {
                    "description": "Optional list of feature keys to exclude",
                    "type": "array",
                    "items": {
                        "type": "string"
                    }
                }
            },
            "required": [
                "default"
            ],
            "additionalProperties": false
        },
        "featuresDisplayOrder": {
            "title": "Feature display order",
            "description": "Ordered array of feature keys for display on front end",
            "type": "array",
            "items": {
                "type": "string"
            }
        },
        "featuresDataOrder": {
            "title": "Feature data order",
            "description": "Ordered array of feature keys for packing and unpacking data",
            "type": "array",
            "items": {
                "type": "string"
            }
        },
        "input-dateCreated": {
            "title": "Date the dataset was created",
            "description": "Format: Month Day, Year. If it's not specified, the date will be set to the upload date. ",
            "type": "string"
        },
        "input-datasets": {
            "title": "Input datasets",
            "description": "Array of subfolder names that point to each dataset in the group. Each subfolder should contain their own `dataset.json`.",
            "type": "array",
            "items": {
                "type": "string"
            }
        },
        "input-image": {
            "title": "Image file",
            "description": "Relative path to the dataset card image file, including filename.",
            "type": "string"
        },
        "input-featuresDataPath": {
            "title": "Feature data path",
            "description": "Relative path to the per cell data json, including filename.",
            "type": "string"
        },
        "input-featureDefsPath": {
            "title": "Feature defs path",
            "description": "Relative path to the feature definition file, including filename.",
            "type": "string"
        },
        "input-viewerSettingsPath": {
            "title": "Viewer settings path",
            "description": "Relative path to image per-channel settings file for the 3d viewer, including filename.",
            "type": "string"
        },
        "input-albumPath": {
            "title": "Album path",
            "description": "Relative path to the album file.",
            "type": "string"
        },
        "processed-dateCreated": {
            "title": "Date the dataset was created",
            "description": "Format: Firebase Timestamp. ",
            "type": "string"
        },
        "processed-datasets": {
            "title": "Input datasets",
            "description": "Array of dateset cards.",
            "type": "array",
            "items": {
                "type": "object",
                "$ref": "dataset-card.schema.json"
            }
        },
        "processed-image": {
            "title": "Image file",
            "description": "Url of the dataset card image file on AWS",
            "type": "string"
        },
        "processed-featuresDataPath": {
            "title": "Feature data path",
            "description": "Url of the features JSON on AWS",
            "type": "string"
        },
        "processed-featureDefsPath": {
            "title": "Feature defs path",
            "description": "Database path to feature definition collection",
            "type": "string"
        },
        "processed-viewerSettingsPath": {
            "title": "Viewer settings path",
            "description": "Url of the per-channel settings file for the 3d viewer on AWS.",
            "type": "string"
        },
        "processed-albumPath": {
            "title": "Album path",
            "description": "Database path to album information.",
            "type": "string"
        },
        "datasetLinks": {
            "title": "Dataset Link",
            "description": "Array of dataset links",
            "type": "array",
            "items": {
                "$ref": "array-items/dataset-link.schema.json",
                "type": "object"
            }
        }
    }
}

JSON Schema for File info

{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "$id": "array-items/file-info.schema.json",
    "title": "File info",
    "description": "File info for one cell, this is the data needed to access images for the cell.",
    "type": "object",
    "additionalProperties": false,
    "properties": {
        "CellId": {
            "description": "unique id for segmented cell",
            "type": "string"
        },
        "FOVId": {
            "description": "Field of view cell came from",
            "type": "string"
        },
        "groupBy": {
            "description": "Id of feature the data is grouped by by default",
            "type": "string"
        },
        "thumbnailPath": {
            "description": "Path to thumbnail image for cell",
            "type": "string"
        },
        "volumeviewerPath": {
            "description": "path to 3d data for cell",
            "type": "string"
        },
        "fovThumbnailPath": {
            "description": "Path to fov thumbnail",
            "type": "string"
        },
        "fovVolumeviewerPath": {
            "description": "Path to the fov 3d data",
            "type": "string"
        },
        "transform": {
            "description": "Transform to apply to the cell",
            "type": "object",
            "additionalProperties": false,
            "properties": {
                "translation": {
                    "description": "Translation to apply to the cell",
                    "type": "array",
                    "items": {
                        "type": "number"
                    }
                },
                "rotation": {
                    "description": "Rotation to apply to the cell, as XYZ Euler angles in radians",
                    "type": "array",
                    "items": {
                        "type": "number"
                    }
                }
            }
        }
    },
    "required": [
        "CellId",
        "FOVId",
        "groupBy",
        "volumeviewerPath"
    ]
}

JSON Schema for Input datasets

{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "$id": "definitions.schema.json",
    "title": "Definitions of dataset properties",
    "type": "object",
    "additionalProperties": false,
    "definitions": {
        "group-title": {
            "title": "Group title",
            "description": "Display name of dataset group.",
            "type": "string"
        },
        "dataset-title": {
            "title": "Dataset title",
            "description": "Display name of dataset.",
            "type": "string"
        },
        "name": {
            "title": "Dataset name",
            "description": "Name of the group (no version number). Lowercase with underscores.",
            "type": "string"
        },
        "index": {
            "title": "Dataset index",
            "description": "Index of dataset in a megaset.",
            "type": "number"
        },
        "publication": {
            "title": "Publication",
            "description": "Publication data",
            "additionalProperties": false,
            "type": "object",
            "properties": {
                "title": {
                    "description": "Article title",
                    "type": "string"
                },
                "url": {
                    "description": "Article link",
                    "type": "string"
                },
                "citation": {
                    "description": "Article journal and date",
                    "type": "string"
                }
            }
        },
        "version": {
            "title": "Version",
            "description": "Version year and number",
            "type": "string"
        },
        "description": {
            "title": "Description",
            "description": "Description of the dataset",
            "type": "string"
        },
        "extra": {
            "title": "Extra",
            "description": "Extra text to display on the card with a callout box",
            "type": "string"
        },
        "link": {
            "title": "Link (deprecated)",
            "description": "Link to website displaying the dataset",
            "type": "string"
        },
        "userData": {
            "title": "User data",
            "description": "Optional display data",
            "type": "object"
        },
        "production": {
            "title": "Is production",
            "description": "Whether this dataset should be shown in production",
            "type": "boolean"
        },
        "thumbnailRoot": {
            "title": "Thumbnail root",
            "description": "Root url for thumbnail images",
            "type": "string"
        },
        "downloadRoot": {
            "title": "Download root",
            "description": "Root url for downloading cell data",
            "type": "string"
        },
        "volumeViewerDataRoot": {
            "title": "VolumeViewer data root",
            "description": "Root url for 3d images",
            "type": "string"
        },
        "selection-settings": {
            "title": "Selection settings",
            "type": "object",
            "properties": {
                "default": {
                    "description": "Default feature key for the setting",
                    "type": "string"
                },
                "exclude": {
                    "description": "Optional list of feature keys to exclude",
                    "type": "array",
                    "items": {
                        "type": "string"
                    }
                }
            },
            "required": [
                "default"
            ],
            "additionalProperties": false
        },
        "featuresDisplayOrder": {
            "title": "Feature display order",
            "description": "Ordered array of feature keys for display on front end",
            "type": "array",
            "items": {
                "type": "string"
            }
        },
        "featuresDataOrder": {
            "title": "Feature data order",
            "description": "Ordered array of feature keys for packing and unpacking data",
            "type": "array",
            "items": {
                "type": "string"
            }
        },
        "input-dateCreated": {
            "title": "Date the dataset was created",
            "description": "Format: Month Day, Year. If it's not specified, the date will be set to the upload date. ",
            "type": "string"
        },
        "input-datasets": {
            "title": "Input datasets",
            "description": "Array of subfolder names that point to each dataset in the group. Each subfolder should contain their own `dataset.json`.",
            "type": "array",
            "items": {
                "type": "string"
            }
        },
        "input-image": {
            "title": "Image file",
            "description": "Relative path to the dataset card image file, including filename.",
            "type": "string"
        },
        "input-featuresDataPath": {
            "title": "Feature data path",
            "description": "Relative path to the per cell data json, including filename.",
            "type": "string"
        },
        "input-featureDefsPath": {
            "title": "Feature defs path",
            "description": "Relative path to the feature definition file, including filename.",
            "type": "string"
        },
        "input-viewerSettingsPath": {
            "title": "Viewer settings path",
            "description": "Relative path to image per-channel settings file for the 3d viewer, including filename.",
            "type": "string"
        },
        "input-albumPath": {
            "title": "Album path",
            "description": "Relative path to the album file.",
            "type": "string"
        },
        "processed-dateCreated": {
            "title": "Date the dataset was created",
            "description": "Format: Firebase Timestamp. ",
            "type": "string"
        },
        "processed-datasets": {
            "title": "Input datasets",
            "description": "Array of dateset cards.",
            "type": "array",
            "items": {
                "type": "object",
                "$ref": "dataset-card.schema.json"
            }
        },
        "processed-image": {
            "title": "Image file",
            "description": "Url of the dataset card image file on AWS",
            "type": "string"
        },
        "processed-featuresDataPath": {
            "title": "Feature data path",
            "description": "Url of the features JSON on AWS",
            "type": "string"
        },
        "processed-featureDefsPath": {
            "title": "Feature defs path",
            "description": "Database path to feature definition collection",
            "type": "string"
        },
        "processed-viewerSettingsPath": {
            "title": "Viewer settings path",
            "description": "Url of the per-channel settings file for the 3d viewer on AWS.",
            "type": "string"
        },
        "processed-albumPath": {
            "title": "Album path",
            "description": "Database path to album information.",
            "type": "string"
        },
        "datasetLinks": {
            "title": "Dataset Link",
            "description": "Array of dataset links",
            "type": "array",
            "items": {
                "$ref": "array-items/dataset-link.schema.json",
                "type": "object"
            }
        }
    }
}

JSON Schema for Manifest

{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "$id": "manifest.schema.json",
    "title": "Manifest",
    "description": "High level data for each dataset that points to where all the data is stored for this dataset.",
    "type": "object",
    "additionalProperties": false,
    "properties": {
        "featuresDataPath": {
            "$ref": "definitions.schema.json#/definitions/processed-featuresDataPath"
        },
        "featureDefsPath": {
            "$ref": "definitions.schema.json#/definitions/processed-featureDefsPath"
        },
        "viewerSettingsPath": {
            "$ref": "definitions.schema.json#/definitions/processed-viewerSettingsPath"
        },
        "albumPath": {
            "$ref": "definitions.schema.json#/definitions/processed-albumPath"
        },
        "thumbnailRoot": {
            "$ref": "definitions.schema.json#/definitions/thumbnailRoot"
        },
        "downloadRoot": {
            "$ref": "definitions.schema.json#/definitions/downloadRoot"
        },
        "volumeViewerDataRoot": {
            "$ref": "definitions.schema.json#/definitions/volumeViewerDataRoot"
        },
        "xAxis": {
            "title": "xAxis settings",
            "description": "Settings for the x axis",
            "type": "object",
            "$ref": "definitions.schema.json#/definitions/selection-settings"
        },
        "yAxis": {
            "title": "yAxis settings",
            "description": "Settings for the y axis",
            "type": "object",
            "$ref": "definitions.schema.json#/definitions/selection-settings"
        },
        "colorBy": {
            "title": "Color settings",
            "description": "Settings for the color by menu",
            "type": "object",
            "$ref": "definitions.schema.json#/definitions/selection-settings"
        },
        "groupBy": {
            "title": "Grouping settings",
            "description": "Settings for the grouping menu",
            "type": "object",
            "$ref": "definitions.schema.json#/definitions/selection-settings"
        },
        "featuresDisplayOrder": {
            "$ref": "definitions.schema.json#/definitions/featuresDisplayOrder"
        },
        "featuresDataOrder": {
            "$ref": "definitions.schema.json#/definitions/featuresDataOrder"
        }
    },
    "required": [
        "featuresDataPath",
        "viewerSettingsPath",
        "albumPath",
        "thumbnailRoot",
        "downloadRoot",
        "volumeViewerDataRoot",
        "xAxis",
        "yAxis",
        "groupBy",
        "colorBy",
        "featuresDisplayOrder",
        "featuresDataOrder"
    ]
}

JSON Schema for Megaset Card

{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "$id": "megaset-card.schema.json",
    "title": "Megaset Card",
    "description": "Data needed to render a megaset card",
    "type": "object",
    "additionalProperties": false,
    "properties": {
        "datasets": {
            "$ref": "definitions.schema.json#/definitions/processed-datasets"
        },
        "dateCreated": {
            "$ref": "definitions.schema.json#/definitions/processed-dateCreated"
        },
        "name": {
            "$ref": "definitions.schema.json#/definitions/name"
        },
        "production": {
            "$ref": "definitions.schema.json#/definitions/production"
        },
        "title": {
            "$ref": "definitions.schema.json#/definitions/group-title"
        },
        "publications": {
            "title": "Publications",
            "description": "Publications associated with the group",
            "type": "array",
            "items": {
                "$ref": "definitions.schema.json#/definitions/publication"
            }
        }
    },
    "required": [
        "datasets",
        "dateCreated",
        "name",
        "production",
        "title"
    ]
}

JSON Schema for Publication

{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "$id": "definitions.schema.json",
    "title": "Definitions of dataset properties",
    "type": "object",
    "additionalProperties": false,
    "definitions": {
        "group-title": {
            "title": "Group title",
            "description": "Display name of dataset group.",
            "type": "string"
        },
        "dataset-title": {
            "title": "Dataset title",
            "description": "Display name of dataset.",
            "type": "string"
        },
        "name": {
            "title": "Dataset name",
            "description": "Name of the group (no version number). Lowercase with underscores.",
            "type": "string"
        },
        "index": {
            "title": "Dataset index",
            "description": "Index of dataset in a megaset.",
            "type": "number"
        },
        "publication": {
            "title": "Publication",
            "description": "Publication data",
            "additionalProperties": false,
            "type": "object",
            "properties": {
                "title": {
                    "description": "Article title",
                    "type": "string"
                },
                "url": {
                    "description": "Article link",
                    "type": "string"
                },
                "citation": {
                    "description": "Article journal and date",
                    "type": "string"
                }
            }
        },
        "version": {
            "title": "Version",
            "description": "Version year and number",
            "type": "string"
        },
        "description": {
            "title": "Description",
            "description": "Description of the dataset",
            "type": "string"
        },
        "extra": {
            "title": "Extra",
            "description": "Extra text to display on the card with a callout box",
            "type": "string"
        },
        "link": {
            "title": "Link (deprecated)",
            "description": "Link to website displaying the dataset",
            "type": "string"
        },
        "userData": {
            "title": "User data",
            "description": "Optional display data",
            "type": "object"
        },
        "production": {
            "title": "Is production",
            "description": "Whether this dataset should be shown in production",
            "type": "boolean"
        },
        "thumbnailRoot": {
            "title": "Thumbnail root",
            "description": "Root url for thumbnail images",
            "type": "string"
        },
        "downloadRoot": {
            "title": "Download root",
            "description": "Root url for downloading cell data",
            "type": "string"
        },
        "volumeViewerDataRoot": {
            "title": "VolumeViewer data root",
            "description": "Root url for 3d images",
            "type": "string"
        },
        "selection-settings": {
            "title": "Selection settings",
            "type": "object",
            "properties": {
                "default": {
                    "description": "Default feature key for the setting",
                    "type": "string"
                },
                "exclude": {
                    "description": "Optional list of feature keys to exclude",
                    "type": "array",
                    "items": {
                        "type": "string"
                    }
                }
            },
            "required": [
                "default"
            ],
            "additionalProperties": false
        },
        "featuresDisplayOrder": {
            "title": "Feature display order",
            "description": "Ordered array of feature keys for display on front end",
            "type": "array",
            "items": {
                "type": "string"
            }
        },
        "featuresDataOrder": {
            "title": "Feature data order",
            "description": "Ordered array of feature keys for packing and unpacking data",
            "type": "array",
            "items": {
                "type": "string"
            }
        },
        "input-dateCreated": {
            "title": "Date the dataset was created",
            "description": "Format: Month Day, Year. If it's not specified, the date will be set to the upload date. ",
            "type": "string"
        },
        "input-datasets": {
            "title": "Input datasets",
            "description": "Array of subfolder names that point to each dataset in the group. Each subfolder should contain their own `dataset.json`.",
            "type": "array",
            "items": {
                "type": "string"
            }
        },
        "input-image": {
            "title": "Image file",
            "description": "Relative path to the dataset card image file, including filename.",
            "type": "string"
        },
        "input-featuresDataPath": {
            "title": "Feature data path",
            "description": "Relative path to the per cell data json, including filename.",
            "type": "string"
        },
        "input-featureDefsPath": {
            "title": "Feature defs path",
            "description": "Relative path to the feature definition file, including filename.",
            "type": "string"
        },
        "input-viewerSettingsPath": {
            "title": "Viewer settings path",
            "description": "Relative path to image per-channel settings file for the 3d viewer, including filename.",
            "type": "string"
        },
        "input-albumPath": {
            "title": "Album path",
            "description": "Relative path to the album file.",
            "type": "string"
        },
        "processed-dateCreated": {
            "title": "Date the dataset was created",
            "description": "Format: Firebase Timestamp. ",
            "type": "string"
        },
        "processed-datasets": {
            "title": "Input datasets",
            "description": "Array of dateset cards.",
            "type": "array",
            "items": {
                "type": "object",
                "$ref": "dataset-card.schema.json"
            }
        },
        "processed-image": {
            "title": "Image file",
            "description": "Url of the dataset card image file on AWS",
            "type": "string"
        },
        "processed-featuresDataPath": {
            "title": "Feature data path",
            "description": "Url of the features JSON on AWS",
            "type": "string"
        },
        "processed-featureDefsPath": {
            "title": "Feature defs path",
            "description": "Database path to feature definition collection",
            "type": "string"
        },
        "processed-viewerSettingsPath": {
            "title": "Viewer settings path",
            "description": "Url of the per-channel settings file for the 3d viewer on AWS.",
            "type": "string"
        },
        "processed-albumPath": {
            "title": "Album path",
            "description": "Database path to album information.",
            "type": "string"
        },
        "datasetLinks": {
            "title": "Dataset Link",
            "description": "Array of dataset links",
            "type": "array",
            "items": {
                "$ref": "array-items/dataset-link.schema.json",
                "type": "object"
            }
        }
    }
}

JSON Schema for Selection settings

{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "$id": "definitions.schema.json",
    "title": "Definitions of dataset properties",
    "type": "object",
    "additionalProperties": false,
    "definitions": {
        "group-title": {
            "title": "Group title",
            "description": "Display name of dataset group.",
            "type": "string"
        },
        "dataset-title": {
            "title": "Dataset title",
            "description": "Display name of dataset.",
            "type": "string"
        },
        "name": {
            "title": "Dataset name",
            "description": "Name of the group (no version number). Lowercase with underscores.",
            "type": "string"
        },
        "index": {
            "title": "Dataset index",
            "description": "Index of dataset in a megaset.",
            "type": "number"
        },
        "publication": {
            "title": "Publication",
            "description": "Publication data",
            "additionalProperties": false,
            "type": "object",
            "properties": {
                "title": {
                    "description": "Article title",
                    "type": "string"
                },
                "url": {
                    "description": "Article link",
                    "type": "string"
                },
                "citation": {
                    "description": "Article journal and date",
                    "type": "string"
                }
            }
        },
        "version": {
            "title": "Version",
            "description": "Version year and number",
            "type": "string"
        },
        "description": {
            "title": "Description",
            "description": "Description of the dataset",
            "type": "string"
        },
        "extra": {
            "title": "Extra",
            "description": "Extra text to display on the card with a callout box",
            "type": "string"
        },
        "link": {
            "title": "Link (deprecated)",
            "description": "Link to website displaying the dataset",
            "type": "string"
        },
        "userData": {
            "title": "User data",
            "description": "Optional display data",
            "type": "object"
        },
        "production": {
            "title": "Is production",
            "description": "Whether this dataset should be shown in production",
            "type": "boolean"
        },
        "thumbnailRoot": {
            "title": "Thumbnail root",
            "description": "Root url for thumbnail images",
            "type": "string"
        },
        "downloadRoot": {
            "title": "Download root",
            "description": "Root url for downloading cell data",
            "type": "string"
        },
        "volumeViewerDataRoot": {
            "title": "VolumeViewer data root",
            "description": "Root url for 3d images",
            "type": "string"
        },
        "selection-settings": {
            "title": "Selection settings",
            "type": "object",
            "properties": {
                "default": {
                    "description": "Default feature key for the setting",
                    "type": "string"
                },
                "exclude": {
                    "description": "Optional list of feature keys to exclude",
                    "type": "array",
                    "items": {
                        "type": "string"
                    }
                }
            },
            "required": [
                "default"
            ],
            "additionalProperties": false
        },
        "featuresDisplayOrder": {
            "title": "Feature display order",
            "description": "Ordered array of feature keys for display on front end",
            "type": "array",
            "items": {
                "type": "string"
            }
        },
        "featuresDataOrder": {
            "title": "Feature data order",
            "description": "Ordered array of feature keys for packing and unpacking data",
            "type": "array",
            "items": {
                "type": "string"
            }
        },
        "input-dateCreated": {
            "title": "Date the dataset was created",
            "description": "Format: Month Day, Year. If it's not specified, the date will be set to the upload date. ",
            "type": "string"
        },
        "input-datasets": {
            "title": "Input datasets",
            "description": "Array of subfolder names that point to each dataset in the group. Each subfolder should contain their own `dataset.json`.",
            "type": "array",
            "items": {
                "type": "string"
            }
        },
        "input-image": {
            "title": "Image file",
            "description": "Relative path to the dataset card image file, including filename.",
            "type": "string"
        },
        "input-featuresDataPath": {
            "title": "Feature data path",
            "description": "Relative path to the per cell data json, including filename.",
            "type": "string"
        },
        "input-featureDefsPath": {
            "title": "Feature defs path",
            "description": "Relative path to the feature definition file, including filename.",
            "type": "string"
        },
        "input-viewerSettingsPath": {
            "title": "Viewer settings path",
            "description": "Relative path to image per-channel settings file for the 3d viewer, including filename.",
            "type": "string"
        },
        "input-albumPath": {
            "title": "Album path",
            "description": "Relative path to the album file.",
            "type": "string"
        },
        "processed-dateCreated": {
            "title": "Date the dataset was created",
            "description": "Format: Firebase Timestamp. ",
            "type": "string"
        },
        "processed-datasets": {
            "title": "Input datasets",
            "description": "Array of dateset cards.",
            "type": "array",
            "items": {
                "type": "object",
                "$ref": "dataset-card.schema.json"
            }
        },
        "processed-image": {
            "title": "Image file",
            "description": "Url of the dataset card image file on AWS",
            "type": "string"
        },
        "processed-featuresDataPath": {
            "title": "Feature data path",
            "description": "Url of the features JSON on AWS",
            "type": "string"
        },
        "processed-featureDefsPath": {
            "title": "Feature defs path",
            "description": "Database path to feature definition collection",
            "type": "string"
        },
        "processed-viewerSettingsPath": {
            "title": "Viewer settings path",
            "description": "Url of the per-channel settings file for the 3d viewer on AWS.",
            "type": "string"
        },
        "processed-albumPath": {
            "title": "Album path",
            "description": "Database path to album information.",
            "type": "string"
        },
        "datasetLinks": {
            "title": "Dataset Link",
            "description": "Array of dataset links",
            "type": "array",
            "items": {
                "$ref": "array-items/dataset-link.schema.json",
                "type": "object"
            }
        }
    }
}

JSON Schema for User data

{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "$id": "definitions.schema.json",
    "title": "Definitions of dataset properties",
    "type": "object",
    "additionalProperties": false,
    "definitions": {
        "group-title": {
            "title": "Group title",
            "description": "Display name of dataset group.",
            "type": "string"
        },
        "dataset-title": {
            "title": "Dataset title",
            "description": "Display name of dataset.",
            "type": "string"
        },
        "name": {
            "title": "Dataset name",
            "description": "Name of the group (no version number). Lowercase with underscores.",
            "type": "string"
        },
        "index": {
            "title": "Dataset index",
            "description": "Index of dataset in a megaset.",
            "type": "number"
        },
        "publication": {
            "title": "Publication",
            "description": "Publication data",
            "additionalProperties": false,
            "type": "object",
            "properties": {
                "title": {
                    "description": "Article title",
                    "type": "string"
                },
                "url": {
                    "description": "Article link",
                    "type": "string"
                },
                "citation": {
                    "description": "Article journal and date",
                    "type": "string"
                }
            }
        },
        "version": {
            "title": "Version",
            "description": "Version year and number",
            "type": "string"
        },
        "description": {
            "title": "Description",
            "description": "Description of the dataset",
            "type": "string"
        },
        "extra": {
            "title": "Extra",
            "description": "Extra text to display on the card with a callout box",
            "type": "string"
        },
        "link": {
            "title": "Link (deprecated)",
            "description": "Link to website displaying the dataset",
            "type": "string"
        },
        "userData": {
            "title": "User data",
            "description": "Optional display data",
            "type": "object"
        },
        "production": {
            "title": "Is production",
            "description": "Whether this dataset should be shown in production",
            "type": "boolean"
        },
        "thumbnailRoot": {
            "title": "Thumbnail root",
            "description": "Root url for thumbnail images",
            "type": "string"
        },
        "downloadRoot": {
            "title": "Download root",
            "description": "Root url for downloading cell data",
            "type": "string"
        },
        "volumeViewerDataRoot": {
            "title": "VolumeViewer data root",
            "description": "Root url for 3d images",
            "type": "string"
        },
        "selection-settings": {
            "title": "Selection settings",
            "type": "object",
            "properties": {
                "default": {
                    "description": "Default feature key for the setting",
                    "type": "string"
                },
                "exclude": {
                    "description": "Optional list of feature keys to exclude",
                    "type": "array",
                    "items": {
                        "type": "string"
                    }
                }
            },
            "required": [
                "default"
            ],
            "additionalProperties": false
        },
        "featuresDisplayOrder": {
            "title": "Feature display order",
            "description": "Ordered array of feature keys for display on front end",
            "type": "array",
            "items": {
                "type": "string"
            }
        },
        "featuresDataOrder": {
            "title": "Feature data order",
            "description": "Ordered array of feature keys for packing and unpacking data",
            "type": "array",
            "items": {
                "type": "string"
            }
        },
        "input-dateCreated": {
            "title": "Date the dataset was created",
            "description": "Format: Month Day, Year. If it's not specified, the date will be set to the upload date. ",
            "type": "string"
        },
        "input-datasets": {
            "title": "Input datasets",
            "description": "Array of subfolder names that point to each dataset in the group. Each subfolder should contain their own `dataset.json`.",
            "type": "array",
            "items": {
                "type": "string"
            }
        },
        "input-image": {
            "title": "Image file",
            "description": "Relative path to the dataset card image file, including filename.",
            "type": "string"
        },
        "input-featuresDataPath": {
            "title": "Feature data path",
            "description": "Relative path to the per cell data json, including filename.",
            "type": "string"
        },
        "input-featureDefsPath": {
            "title": "Feature defs path",
            "description": "Relative path to the feature definition file, including filename.",
            "type": "string"
        },
        "input-viewerSettingsPath": {
            "title": "Viewer settings path",
            "description": "Relative path to image per-channel settings file for the 3d viewer, including filename.",
            "type": "string"
        },
        "input-albumPath": {
            "title": "Album path",
            "description": "Relative path to the album file.",
            "type": "string"
        },
        "processed-dateCreated": {
            "title": "Date the dataset was created",
            "description": "Format: Firebase Timestamp. ",
            "type": "string"
        },
        "processed-datasets": {
            "title": "Input datasets",
            "description": "Array of dateset cards.",
            "type": "array",
            "items": {
                "type": "object",
                "$ref": "dataset-card.schema.json"
            }
        },
        "processed-image": {
            "title": "Image file",
            "description": "Url of the dataset card image file on AWS",
            "type": "string"
        },
        "processed-featuresDataPath": {
            "title": "Feature data path",
            "description": "Url of the features JSON on AWS",
            "type": "string"
        },
        "processed-featureDefsPath": {
            "title": "Feature defs path",
            "description": "Database path to feature definition collection",
            "type": "string"
        },
        "processed-viewerSettingsPath": {
            "title": "Viewer settings path",
            "description": "Url of the per-channel settings file for the 3d viewer on AWS.",
            "type": "string"
        },
        "processed-albumPath": {
            "title": "Album path",
            "description": "Database path to album information.",
            "type": "string"
        },
        "datasetLinks": {
            "title": "Dataset Link",
            "description": "Array of dataset links",
            "type": "array",
            "items": {
                "$ref": "array-items/dataset-link.schema.json",
                "type": "object"
            }
        }
    }
}

What the data looks like in the database after processing

Cell Feature Database Specification

Cell Feature Database Specification.dataset-descriptions

Cell Feature Database Specification.manifests

Cell Feature Database Specification.dataset-data

Cell Feature Database Specification.cell-data

Cell Feature Database Specification.measured-features

Condensed measured feature

array-items/condensed-measured-feature.f

array-items/condensed-measured-feature.p

array-items/condensed-measured-feature.t

array-items/condensed-measured-feature.i

Condensed measured features JSON

Dataset Card

dataset-card.title

dataset-card.name

dataset-card.version

dataset-card.description

dataset-card.extra

dataset-card.image

dataset-card.link

dataset-card.userData

dataset-card.production

dataset-card.index

dataset-card.datasetLinks

Dataset Description Collection

Dataset Link

array-items/dataset-link.date

array-items/dataset-link.title

array-items/dataset-link.link

Discrete feature option

array-items/discrete-feature-option.color

array-items/discrete-feature-option.name

array-items/discrete-feature-option.key

Discrete feature options

Feature data order

Feature Definition

feature-def.displayName

feature-def.description

feature-def.tooltip

feature-def.unit

feature-def.key

feature-def.discrete

feature-def.options

Feature display order

File info

array-items/file-info.CellId

array-items/file-info.FOVId

array-items/file-info.groupBy

array-items/file-info.thumbnailPath

array-items/file-info.volumeviewerPath

array-items/file-info.fovThumbnailPath

array-items/file-info.fovVolumeviewerPath

array-items/file-info.transform

Input datasets

Manifest

manifest.featuresDataPath

manifest.featureDefsPath

manifest.viewerSettingsPath

manifest.albumPath

manifest.thumbnailRoot

manifest.downloadRoot

manifest.volumeViewerDataRoot

manifest.xAxis

manifest.yAxis

manifest.colorBy

manifest.groupBy

manifest.featuresDisplayOrder

manifest.featuresDataOrder

Megaset Card

megaset-card.datasets

megaset-card.dateCreated

megaset-card.name

megaset-card.production

megaset-card.title

megaset-card.publications

Publication

publication.title

publication.url

publication.citation