How to hand off a dataset

1. Create the files

(the only file names that matters are dataset.json)

For a single dataset:

Create a folder with 5 files:

dataset.json
feature_analysis.json or .zip depending on the size
feature_defs.json
images.json
card-cover.png (for display on the homepage)

For a group of datasets, ie a Megaset

Create a folder with 1 file and one folder per dataset. Each folder should have the same 5 files listed above.

Megaset Folder/

dataset.json

dataset-1/

dataset.json
… the other 4 files listed above

dataset-2/

dataset.json
… the other 4 files listed above

Refer to Megaset for more information.

2. Make a PR to this repo with your dataset folder.

Full Documentation

3D Viewer Settings

Settings for the 3D viewer

Table 1. `3D Viewer Settings` Properties
	Type	Description	Required
maskChannelName	`string`	Name of channel to use as mask, applied to all other enabled channels. Generally this would be a segmentation channel or a channel with binary data. If omitted, then no masking will be available.	No
groups	`object` `[]`	Collection of named channel groupings. If omitted, then there will be a single group called "Channels".	No

Additional properties are not allowed.

JSON schema: images.schema.json

images.maskChannelName

Name of channel to use as mask, applied to all other enabled channels. Generally this would be a segmentation channel or a channel with binary data. If omitted, then no masking will be available.

Type: string
Required: No

images.groups

Collection of named channel groupings. If omitted, then there will be a single group called "Channels".

Type: object []
Required: No

Cell Feature Dataset Handoff Specification

all the files needed for handoff

Table 2. `Cell Feature Dataset Handoff Specification` Properties
	Type	Description	Required
megaset	`input-megaset`	File that describes a group of datasets (ie a 'Megaset'). Should be at the highest level, and the datasets nested in their own folders. This file needs to be named `dataset.json`	No
dataset	`input-dataset-info`	File containing the data needed to process a dataset. If single dataset, should be at the highest folder level. If one of many in a group of datasets, should be in a subfolder pointed to by the megaset JSON `datasets` array. Should be named `dataset.json`	✓ Yes
feature-defs	`feature-def` `[]`	File that describes the measured feature definitions. Is an array of feature definitions.	✓ Yes
measured-features	`array-items/input-measured-features` `[]`	Input file containing measured features and file info for each image.	✓ Yes
images	`images`	Settings for the 3D viewer	No

Additional properties are not allowed.

JSON schema: input-dataset.schema.json

Cell Feature Dataset Handoff Specification.megaset

File that describes a group of datasets (ie a 'Megaset'). Should be at the highest level, and the datasets nested in their own folders. This file needs to be named dataset.json

Type: input-megaset
Required: No

Cell Feature Dataset Handoff Specification.dataset

File containing the data needed to process a dataset. If single dataset, should be at the highest folder level. If one of many in a group of datasets, should be in a subfolder pointed to by the megaset JSON datasets array. Should be named dataset.json

Type: input-dataset-info
Required: ✓ Yes

Cell Feature Dataset Handoff Specification.feature-defs

File that describes the measured feature definitions. Is an array of feature definitions.

Type: feature-def []
Required: ✓ Yes

Cell Feature Dataset Handoff Specification.measured-features

Input file containing measured features and file info for each image.

Type: array-items/input-measured-features []
Required: ✓ Yes

Cell Feature Dataset Handoff Specification.images

Settings for the 3D viewer

Type: images
Required: No

Dataset Link

Schema for each single dataset

Table 3. `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 4. `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 5. `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 6. `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

Input dataset info `dataset.json`

Table 7. Input dataset info `dataset.json` 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
image	`string`	Relative path to the dataset card image file, including filename.	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
featuresDataPath	`string`	Relative path to the per cell data json, including filename.	✓ Yes
featureDefsPath	`string`	Relative path to the feature definition file, including filename.	No
viewerSettingsPath	`string`	Relative path to image per-channel settings file for the 3d viewer, including filename.	No
albumPath	`string`	Relative path to the album file.	No
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
datasetLinks	`array-items/dataset-link` `[]`	Array of dataset links	No

Additional properties are not allowed.

JSON schema: input-dataset-info.schema.json

input-dataset-info.title

Display name of dataset.

Type: string
Required: ✓ Yes

input-dataset-info.name

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

Type: string
Required: ✓ Yes

input-dataset-info.version

Version year and number

Type: string
Required: ✓ Yes

input-dataset-info.description

Description of the dataset

Type: string
Required: ✓ Yes

input-dataset-info.image

Relative path to the dataset card image file, including filename.

Type: string
Required: No

input-dataset-info.link

Link to website displaying the dataset

Type: string
Required: No

input-dataset-info.userData

Optional display data

Type: userData
Required: No

input-dataset-info.production

Whether this dataset should be shown in production

Type: boolean
Required: No

input-dataset-info.featuresDataPath

Relative path to the per cell data json, including filename.

Type: string
Required: ✓ Yes

input-dataset-info.featureDefsPath

Relative path to the feature definition file, including filename.

Type: string
Required: No

input-dataset-info.viewerSettingsPath

Relative path to image per-channel settings file for the 3d viewer, including filename.

Type: string
Required: No

input-dataset-info.albumPath

Relative path to the album file.

Type: string
Required: No

input-dataset-info.thumbnailRoot

Root url for thumbnail images

Type: string
Required: ✓ Yes

input-dataset-info.downloadRoot

Root url for downloading cell data

Type: string
Required: ✓ Yes

input-dataset-info.volumeViewerDataRoot

Root url for 3d images

Type: string
Required: ✓ Yes

input-dataset-info.xAxis

Type: selection-settings
Required: ✓ Yes

input-dataset-info.yAxis

Type: selection-settings
Required: ✓ Yes

input-dataset-info.colorBy

Type: selection-settings
Required: ✓ Yes

input-dataset-info.groupBy

Type: selection-settings
Required: ✓ Yes

input-dataset-info.featuresDisplayOrder

Ordered array of feature keys for display on front end

Type: string []
Required: ✓ Yes

input-dataset-info.featuresDataOrder

Ordered array of feature keys for packing and unpacking data

Type: string []
Required: ✓ Yes

input-dataset-info.datasetLinks

Array of dataset links

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

Input datasets

Array of subfolder names that point to each dataset in the group. Each subfolder should contain their own dataset.json.

Type: string
JSON schema: definitions.schema.json

Input Megaset `dataset.json`

File that describes a group of datasets (ie a 'Megaset'). Should be at the highest level, and the datasets nested in their own folders. This file needs to be named dataset.json

Table 8. Input Megaset `dataset.json` Properties
	Type	Description	Required
title	`string`	Display name of dataset group.	✓ Yes
name	`string`	Name of the group (no version number). Lowercase with underscores.	✓ Yes
datasets	`string` `[]`	Array of subfolder names that point to each dataset in the group. Each subfolder should contain their own `dataset.json`.	✓ Yes
dateCreated	`string`	Format: Month Day, Year. If it’s not specified, the date will be set to the upload date.	No
publications	`publication` `[]`	Publications associated with the group	No

Additional properties are not allowed.

JSON schema: input-megaset.schema.json

input-megaset.title

Display name of dataset group.

Type: string
Required: ✓ Yes

input-megaset.name

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

Type: string
Required: ✓ Yes

input-megaset.datasets

Array of subfolder names that point to each dataset in the group. Each subfolder should contain their own dataset.json.

Type: string []
Required: ✓ Yes

input-megaset.dateCreated

Format: Month Day, Year. If it’s not specified, the date will be set to the upload date.

Type: string
Required: No

input-megaset.publications

Publications associated with the group

Type: publication []
Required: No

measured features JSON

Input file containing measured features and file info for each image.

Type: array-items/input-measured-features
JSON schema: input-measured-features-doc.schema.json

Publication

Publication data

Table 9. `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 10. `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

The measured features and fileInfo for one image

Per data point object. The measured features JSON is an array of these objects.

Table 11. `The measured features and fileInfo for one image` Properties
	Type	Description	Required
file_info	`(string or object)[7-8]`	Ordered array of file info: [id, parentId, id of default group, thumbnail path, volume viewer path, parent thumbnail path, parent volume viewer path]. Any of these can be empty strings if they aren’t applicable, but the array needs to be at least 7 items long (8 if including the translation and rotation)	✓ Yes
features	`(number or string)[]`	Ordered array of measured features. Needs to match the order of featuresDataOrder	✓ Yes

Additional properties are not allowed.

JSON schema: array-items/input-measured-features.schema.json

array-items/input-measured-features.file_info

Ordered array of file info: [id, parentId, id of default group, thumbnail path, volume viewer path, parent thumbnail path, parent volume viewer path]. Any of these can be empty strings if they aren’t applicable, but the array needs to be at least 7 items long (8 if including the translation and rotation)

Type: (string or object)[7-8]
- Each element in the array must be one of the following values:
Required: ✓ Yes

array-items/input-measured-features.features

Ordered array of measured features. Needs to match the order of featuresDataOrder

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

User data

Optional display data

Additional properties are allowed.

JSON schema: definitions.schema.json

Appendix

JSON Schema for 3D Viewer Settings

{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "$id": "images.schema.json",
    "title": "3D Viewer Settings",
    "description": "Settings for the 3D viewer",
    "type": "object",
    "additionalProperties": false,
    "properties": {
        "maskChannelName": {
            "description": "Name of channel to use as mask, applied to all other enabled channels. Generally this would be a segmentation channel or a channel with binary data.  If omitted, then no masking will be available.",
            "type": "string"
        },
        "groups": {
            "description": "Collection of named channel groupings. If omitted, then there will be a single group called \"Channels\".",
            "type": "array",
            "items": {
                "title": "3D Viewer Channel Group",
                "description": "Settings for a grouping of channels for the 3D viewer",
                "type": "object",
                "properties": {
                    "name":{
                        "description": "Name of the channel group",
                        "type":"string"
                    },
                    "channels": {
                        "description": "Collection of channel settings in the group",
                        "type": "array",
                        "items": {
                            "title": "Channel Settings",
                            "description": "Default 3D Viewer per-channel settings",
                            "type": "object",
                            "properties": {
                                "name": {
                                    "description": "Displayed name of the channel. If \"match\" is omitted, then this must be an actual channel name in the image.",
                                    "type": "string"
                                },
                                "match": {
                                    "description": "Regular expression, or List of Regular expressions to match channel names.",
                                    "anyOf": [
                                        {
                                            "type": "array",
                                            "items": {
                                                "type": "string"
                                            }
                                        },
                                        {
                                            "type":"string"
                                        }
                                    ]
                                },
                                "color": {
                                    "description": "Color to use for the channel. Must be a 6 digit hex value of format RRGGBB",
                                    "type": "string",
                                    "pattern": "^[0-9A-Fa-f]{6}$"
                                },
                                "enabled": {
                                    "description": "Whether the channel should be enabled (visible) by default",
                                    "type": "boolean"
                                },
                                "lut": {
                                    "description": "Min and max threshold values to use for this channel.  If omitted, viewer default will be used. Prefix with p for percentile, or m for percentage of median. E.g. m105 is 105% of the median intensity. p98 is the 98th percentile intensity. Plain number is interpreted as raw intensity value (0..255 max)",
                                    "type": "array",
                                    "maxItems": 2,
                                    "minItems": 2,
                                    "items": {
                                        "type": "string",
                                        "pattern": "^[pm0-9]+(\\.[0-9]+)?$"
                                    }
                                }
                            }
                        }
                    }
                }
            }
        }
    }
}

JSON Schema for Cell Feature Dataset Handoff Specification

{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "$id": "input-dataset.schema.json",
    "title": "Cell Feature Dataset Handoff Specification",
    "description": "all the files needed for handoff",
    "type": "object",
    "additionalProperties": false,
    "properties": {
        "megaset": {
            "$ref": "input-megaset.schema.json"
        },
        "dataset": {
            "$ref": "input-dataset-info.schema.json"
        },
        "feature-defs": {
            "title": "Feature definitions `feature-defs.json`",
            "description": "File that describes the measured feature definitions. Is an array of feature definitions.",
            "type": "array",
            "items": {
                "$ref": "feature-def.schema.json"
            }
        },
        "measured-features": {
            "$ref": "input-measured-features-doc.schema.json"
        },
        "images": {
            "title": "3D Viewer settings `images.json`",
            "description": "File that contains the 3D viewer settings. These are settings consistent with the type of images being displayed.",
            "$ref": "images.schema.json"
        }
    },
    "required": [
        "dataset",
        "feature-defs",
        "measured-features"
    ]
}

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 Input dataset info `dataset.json`

{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "$id": "input-dataset-info.schema.json",
    "title": "Input dataset info `dataset.json`",
    "description": "File containing the data needed to process a dataset. If single dataset, should be at the highest folder level. If one of many in a group of datasets, should be in a subfolder pointed to by the megaset JSON `datasets` array. Should be named `dataset.json`",
    "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"
        },
        "image": {
            "$ref": "definitions.schema.json#/definitions/input-image"
        },
        "link": {
            "$ref": "definitions.schema.json#/definitions/link"
        },
        "userData": {
            "$ref": "definitions.schema.json#/definitions/userData"
        },
        "production": {
            "$ref": "definitions.schema.json#/definitions/production"
        },
        "featuresDataPath": {
            "$ref": "definitions.schema.json#/definitions/input-featuresDataPath"
        },
        "featureDefsPath": {
            "$ref": "definitions.schema.json#/definitions/input-featureDefsPath"
        },
        "viewerSettingsPath": {
            "$ref": "definitions.schema.json#/definitions/input-viewerSettingsPath"
        },
        "albumPath": {
            "$ref": "definitions.schema.json#/definitions/input-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": {
            "$ref": "definitions.schema.json#/definitions/featuresDataOrder"
        },
        "datasetLinks":{
            "$ref": "definitions.schema.json#/definitions/datasetLinks"
        }
    },
    "required": [
        "title",
        "version",
        "name",
        "description",
        "featuresDataPath",
        "thumbnailRoot",
        "downloadRoot",
        "volumeViewerDataRoot",
        "xAxis",
        "yAxis",
        "groupBy",
        "colorBy",
        "featuresDisplayOrder",
        "featuresDataOrder"
    ]
}

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 Input Megaset `dataset.json`

{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "$id": "input-megaset.schema.json",
    "title": "Input Megaset `dataset.json`",
    "description": "File that describes a group of datasets (ie a 'Megaset'). Should be at the highest level, and the datasets nested in their own folders. This file needs to be named `dataset.json`",
    "type": "object",
    "additionalProperties": false,
    "properties": {
        "title": {
            "$ref": "definitions.schema.json#/definitions/group-title"
        },
        "name": {
            "$ref": "definitions.schema.json#/definitions/name"
        },
        "datasets": {
            "type": "array",
            "$ref": "definitions.schema.json#/definitions/input-datasets",
            "uniqueItems": true
        },
        "dateCreated": {
            "$ref": "definitions.schema.json#/definitions/input-dateCreated"
        },
        "publications": {
            "title": "Publications",
            "description": "Publications associated with the group",
            "type": "array",
            "items": {
                "$ref": "definitions.schema.json#/definitions/publication"
            }
        }
    },
    "required": [
        "title",
        "name",
        "datasets"
    ]
}

JSON Schema for measured features JSON

{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "$id": "input-measured-features-doc.schema.json",
    "title": "measured features JSON",
    "description": "Input file containing measured features and file info for each image.",
    "type": "array",
    "items": {
        "$ref": "array-items/input-measured-features.schema.json"
    }
}

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 The measured features and fileInfo for one image

{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "$id": "array-items/input-measured-features.schema.json",
    "title": "The measured features and fileInfo for one image",
    "description": "Per data point object. The measured features JSON is an array of these objects.",
    "additionalProperties": false,
    "type": "object",
    "properties": {
        "file_info": {
            "description": "Ordered array of file info: [id, parentId, id of default group, thumbnail path, volume viewer path, parent thumbnail path, parent volume viewer path]. Any of these can be empty strings if they aren't applicable, but the array needs to be at least 7 items long (8 if including the translation and rotation)",
            "type": "array",
            "items": {
                "anyOf": [
                    {
                        "type": "string"
                    },
                    {
                        "type": "object",
                        "properties": {
                            "rotation": {
                                "type": "array",
                                "maxItems": 3,
                                "minItems": 3,
                                "items": {
                                    "type": "number"
                                }
                            },
                            "translation": {
                                "type": "array",
                                "maxItems": 3,
                                "minItems": 3,
                                "items": {
                                    "type": "number"
                                }
                            }
                        }
                    }
                ]
            },
            "minItems": 7,
            "maxItems": 8
        },
        "features": {
            "description": "Ordered array of measured features. Needs to match the order of featuresDataOrder",
            "type": "array",
            "items": {
                "anyOf": [
                    {
                        "type": "number"
                    },
                    {
                        "type": "string",
                        "pattern": "[NaN]"
                    }
                ]
            }
        }
    },
    "required": [
        "file_info",
        "features"
    ]
}

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"
            }
        }
    }
}

How to hand off a dataset

1. Create the files

For a single dataset:

For a group of datasets, ie a Megaset

2. Make a PR to this repo with your dataset folder.

Full Documentation

3D Viewer Settings

images.maskChannelName

images.groups

Cell Feature Dataset Handoff Specification

Cell Feature Dataset Handoff Specification.megaset

Cell Feature Dataset Handoff Specification.dataset

Cell Feature Dataset Handoff Specification.feature-defs

Cell Feature Dataset Handoff Specification.measured-features

Cell Feature Dataset Handoff Specification.images

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

Input dataset info dataset.json

input-dataset-info.title

input-dataset-info.name

input-dataset-info.version

input-dataset-info.description

input-dataset-info.image

input-dataset-info.link

input-dataset-info.userData

input-dataset-info.production

input-dataset-info.featuresDataPath

input-dataset-info.featureDefsPath

input-dataset-info.viewerSettingsPath

input-dataset-info.albumPath

input-dataset-info.thumbnailRoot

input-dataset-info.downloadRoot

input-dataset-info.volumeViewerDataRoot

input-dataset-info.xAxis

input-dataset-info.yAxis

input-dataset-info.colorBy

input-dataset-info.groupBy

input-dataset-info.featuresDisplayOrder

input-dataset-info.featuresDataOrder

input-dataset-info.datasetLinks

Input datasets

Input Megaset dataset.json

input-megaset.title

input-megaset.name

input-megaset.datasets

input-megaset.dateCreated

input-megaset.publications

measured features JSON

Publication

publication.title

publication.url

publication.citation

Selection settings

selection-settings.default

selection-settings.exclude

The measured features and fileInfo for one image

array-items/input-measured-features.file_info

array-items/input-measured-features.features

User data

Appendix

JSON Schema for 3D Viewer Settings

JSON Schema for Cell Feature Dataset Handoff Specification

JSON Schema for Dataset Link

Input dataset info `dataset.json`

Input Megaset `dataset.json`

JSON Schema for Input dataset info `dataset.json`

JSON Schema for Input Megaset `dataset.json`