JSON API

Overview

The OMERO JSON API described here provides create, read, update and delete access to an underlying OMERO server. It is implemented as a Django app named api in the OMERO.web framework.

Omero-marshal and Projection-based APIs

The majority of the API URLs use omero-marshal to generate JSON dictionaries from OMERO model objects. All these URLs are under the m prefix:

<server>/api/v0/m/

The webclient currently uses a small number of URLs to perform customized queries for browsing Project, Dataset and Image hierarchies. These queries use projections and typically load a subset of fields for OMERO objects in order to improve performance for large data counts. These will be made available under the p prefix in future releases but are not yet supported.

<server>/api/v0/p/

Versioning

The JSON API uses major and minor version numbers to reflect breaking and non-breaking changes respectively. Non-breaking changes include simple addition of attributes to JSON data or addition of new URLs. The API version is not tied to the version of OMERO.server.

The major version is included in the URL such as /v0/ whereas the full version number can be found in the header:

X-OMERO-ApiVersion: 0.1

JSON format

The JSON objects generated by omero-marshal are defined by the OME-Model. The OMERO model closely follows the OME schema but is not identical. In the cases where OMERO-specific fields are included, these will be prefixed by omero:. For example, omero:details specifies the owner, group and permissions of each object in OMERO. JSON objects also include an @id of the object in the OMERO database and a @type that specifies the OME Schema used to generate it such as http://www.openmicroscopy.org/Schemas/OME/2016-06#Project.

All the fields of the OMERO model object will be included in the JSON except those that are null, which will be omitted. Where supported, modifying the JSON object and saving this back to OMERO will update the object accordingly.

URLs in JSON

URLs are included in JSON objects using keys with the url: prefix. URLs are added for related objects to facilitate exploration of the API in a browser. You may find that a JSON formatting plugin for your browser improves both the presentation and navigation of JSON data.

Loading of linked objects

In most cases the API loads only the requested objects along with their omero:details. For example, /api/v0/m/projects/ loads Projects but does not also load their child Datasets. However, it is sometimes useful to load a number of closely related objects. For example, loading Images also loads their Pixels data (but not Channels) and loading Wells also loads WellSamples (fields) and Images (but not Pixels). The number of objects loaded when listing Images or Wells is kept to a minimum to avoid requesting too much data. This restriction is relaxed when a single Image or Well is loaded. For example, loading a single Image will also load Channels.

Normalizing Experimenters and Groups

When returning a list of JSON objects that each contain omero:details with owner and group data, these will typically be nested many times within the list. In order to avoid this duplication, we can remove objects from within each omero:details and place them under top-level experimenters and experimenterGroups lists. You can specify this with the ?normalize=true query parameter. N.B.: Currently this normalizing will only apply to the top-level objects being listed, such as Projects, Datasets and Images. Where child objects are also loaded (for example Pixels within an Image), the omero:details of these objects will not be affected by the ?normalize=true parameter.

Child counts

For container objects such as Projects, Datasets and Screens it is often useful to know the number of children within them. This can be specified with ?childCount=true parameter. This will add an omero:childCount value to the JSON data.

Filtering by Owner and Group

Most data in OMERO has an Owner and is assigned to a permissions Group. By default, queries will return data from all owners across all groups that are accessible to the current user. Use the query strings to filter by owner and/or group:

/api/v0/m/projects/?owner=3&group=5

When you are retrieving data using an object ID you will not need to filter by group since all the data will be in the same group. For example, Datasets in a specified Project will all be in the same group as the Project.

Error handling

Errors will result in responses with an appropriate status and may include JSON content with a message to provide more information:

  • 404 Not Found: Caused by an invalid URL or when a specified object cannot be found in OMERO.

  • 400 Bad Request: May be caused by invalid query parameters or submitting invalid JSON content. For example, ?limit=foo will give a response of:

    {"message": "invalid literal for int() with base 10: 'foo'"}

  • 405 Method Not Allowed: Returned if you try to use the wrong http method for a url, such as POST to /api/v0/m/projects/. It can also be caused by trying to create or update an unsupported object, such as an Image.

  • 500 Internal Server Error: Generated from any unhandled exceptions. See the message returned and check whether a stacktrace is also included.

Getting started

You may find this example python script useful. It uses the python requests library to connect to the JSON api, login, query data, create and delete Projects. These steps are covered in more detail below.

For an example how to use the API with Java, see JSONClient.java.

List supported versions

You need to find which versions of the API are supported by your server, as described above. These are provided by the base URL:

GET     /api/

Response

{
  "data": [
    {
      "version": "0",
      "url:base": "http://<server>/api/v0/"
    }
  ]
}

List starting URLs

The base URL for the chosen version will list a number of URLs for logging on and getting started.

GET     /api/v0/

Response

{
  "url:login": "http://<server>/api/v0/login/",
  "url:save": "http://<server>/api/v0/m/save/",
  "url:projects": "http://<server>/api/v0/m/projects/",
  "url:plates": "http://<server>/api/v0/m/plates/",
  "url:datasets": "http://<server>/api/v0/m/datasets/",
  "url:token": "http://<server>/api/v0/token/",
  "url:schema": "http://www.openmicroscopy.org/Schemas/OME/2016-06",
  "url:screens": "http://<server>/api/v0/m/screens/",
  "url:servers": "http://<server>/api/v0/servers/",
  "url:images": "http://<server>/api/v0/m/images/"
}

List available OMERO servers

Your API may allow you to connect to several different OMERO servers.

GET     /api/v0/servers/

Response

{
  "data": [
    {
      "host": "<server>",
      "server": "omero",
      "id": 1,
      "port": 4064
    }
  ]
}

Get CSRF token

In order to prevent CSRF attacks, CSRF tokens are required for any POST, PUT and DELETE requests. You will need to obtain a CSRF token for your session and use it for all subsequent requests in that session. You can obtain this from the csrftoken cookie of any request or from the following URL:

GET     /api/v0/token/

Response

{
  "data": "eNoVq528bOqlhQqbCzKuviODTRX3PUO2"
}

Login

You can login to create an OMERO session. You must also include the CSRF token, either in the POST parameters as csrfmiddlewaretoken or in the session header as X-CSRFToken.

The EventContext for this session will be returned to you.

POST    /api/v0/login/

Parameters

Name                  Type        Description
------------------------------------------------------------------
server                Number      ID of the server
username              String      User's username
password              String      User's password
csrfmiddlewaretoken   String      CSRF token (can be provided in header)

Response

{
  "eventContext": {
    "userName": "ben",
    "eventId": -1,
    "sessionUuid": "0b30ee4a-c0b2-4b0f-9c61-f48b31bcad8c",
    "eventType": "User",
    "userId": 3,
    "sessionId": 171319,
    "groupName": "Nevis Lab",
    "isAdmin": False,
    "memberOfGroups": [5, 1, 4],
    "leaderOfGroups": [],
    "groupId": 5
  },
  "success": true
}

Projects, Datasets and Images

OMERO organizes Images in two types of many-to-many hierarchy: screen/plate/[run]/well/image for HCS data and project/dataset/image for other data. Plates, Datasets and Images can also be Orphaned if not contained within any parent container.

Parameters

These query parameters are used by many queries below:

Name        Type        Description
------------------------------------------------------------------
offset      Number      Pagination offset. The default is 0

limit       Number      The size of each page. The default is 200

normalize   Boolean     Place Experimenters and Groups into top-level lists instead
                        of nesting within objects
childCount  Boolean     Use ?childCount=true to include an omero:childCount attribute
                        for container objects
owner       Number      Filter by Experimenter ID

group       Number      Filter by Group ID

List Projects

Parameters

Name        Type        Description
------------------------------------------------------------------
dataset     Number      Filter Projects by child Dataset ID

These query parameters are also supported (see above):

offset, limit, owner, group, childCount, normalize

GET     /api/v0/m/projects/

Response

{
  "data": [
    {
      "Name": "New data",
      "Description": "Example Project",
      "url:project": "http://server.openmicroscopy.org/api/v0/m/projects/11601/",
      "url:datasets": "http://server.openmicroscopy.org/api/v0/m/projects/11601/datasets/",
      "@id": 11601,
      "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project",
      "omero:details": {
        "owner": {
          "UserName": "ben",
          "FirstName": "Ben",
          "MiddleName": "",
          "omero:details": {
            "@type": "TBD#Details",
            "permissions": {
              "isUserWrite": false,
              "isWorldWrite": false,
              "canDelete": false,
              "isWorldRead": false,
              "perm": "------",
              "canEdit": false,
              "canAnnotate": false,
              "isGroupAnnotate": false,
              "isGroupWrite": false,
              "canLink": false,
              "isUserRead": false,
              "@type": "TBD#Permissions",
              "isGroupRead": false
            }
          },
          "Email": "",
          "LastName": "Nevis",
          "@id": 0,
          "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter"
        },
        "group": {
          "omero:details": {
            "@type": "TBD#Details",
            "permissions": {
              "isUserWrite": true,
              "isWorldWrite": false,
              "canDelete": false,
              "isWorldRead": false,
              "perm": "rwra--",
              "canEdit": false,
              "canAnnotate": false,
              "isGroupAnnotate": true,
              "isGroupWrite": false,
              "canLink": false,
              "isUserRead": true,
              "@type": "TBD#Permissions",
              "isGroupRead": true
            }
          },
          "@id": 5,
          "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup",
          "Name": "read-ann"
        },
        "@type": "TBD#Details",
        "permissions": {
          "isUserWrite": true,
          "isWorldWrite": false,
          "canDelete": false,
          "isWorldRead": false,
          "perm": "rwra--",
          "canEdit": false,
          "canAnnotate": true,
          "isGroupAnnotate": true,
          "isGroupWrite": false,
          "canLink": false,
          "isUserRead": true,
          "@type": "TBD#Permissions",
          "isGroupRead": true
        }
      }
    }
  ]
}

Get a single Project

GET   /api/v0/m/projects/{project_id}/

Response

{
  "data": {
    "@id": 3872,
    "Name": "RNAi experiments",
    "Description": "Knockout assays",
    "url:datasets": "http://server.openmicroscopy.org/api/v0/m/projects/3872/datasets/",
    "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project",
    "omero:details": {
      # omitted for brevity
    }
  }
}

List Datasets

Parameters

Name        Type        Description
------------------------------------------------------------------
project     Number      Filter Datasets by parent Project ID

image       Number      Filter Datasets by child Image ID

orphaned    Boolean     Find Datasets that are not in any Project

These query parameters are also supported (see above):

offset, limit, owner, group, childCount, normalize

GET     /api/v0/m/datasets/

Response

{
  "data": [
    {
      "Name": "Test data",
      "Description": "This is the Dataset description",
      "url:dataset": "http://server.openmicroscopy.org/api/v0/m/dataset/112/",
      "url:images": "http://server.openmicroscopy.org/api/v0/m/datasets/112/images/",
      "url:projects": "http://server.openmicroscopy.org/api/v0/m/datasets/112/projects/",
      "@id": 112,
      "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project",
      "omero:details": {
        # omitted for brevity
      }
    }
  ]
}

Datasets in a Project

Datasets can be filtered by parent Project using the ?project=id query string but you can also show Datasets in a Project using this URL:

GET     /api/v0/m/projects/{project_id}/datasets/

Get a single Dataset

GET   /api/v0/m/datasets/{dataset_id}/

Response

{
  "data": {
    "@id": 9702,
    "Name": "My data",
    "Description": "An example set",
    "url:images": "http://server.openmicroscopy.org/api/v0/m/datasets/9702/images/",
    "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Dataset",
    "omero:details": {
      # omitted for brevity
    }
  }
}

List Images

When Images are listed, their Pixels object is also loaded, which includes dimensions and pixel sizes of the Image. When a single Image is retrieved, the Channels data is additionally loaded.

Parameters

Name        Type        Description
------------------------------------------------------------------
dataset     Number      Filter Images by parent Dataset ID

orphaned    Boolean     Find Images that are not in any Dataset or Well

These query parameters are also supported (see above):

offset, limit, owner, group, normalize

GET     /api/v0/m/images/

Response

{
  "data": [
    {
      "@id": 16783,
      "Name": "CFP_AurB_R3D.dv",
      "AcquisitionDate": 1235730332000,
      "omero:details": {
        # omitted for brevity
      },
      "url:image": "http://server.openmicroscopy.org/api/v0/m/images/16783/",
      "Pixels": {
        "@id": 12801,
        "SizeX": 512,
        "SizeY": 512,
        "SizeZ": 29,
        "SizeC": 2,
        "SizeT": 1,
        "PhysicalSizeX": {
          "Symbol": "µm",
          "Value": 0.12698,
          "@type": "TBD#LengthI",
          "Unit": "MICROMETER"
        },
        "PhysicalSizeY": {
          "Symbol": "µm",
          "Value": 0.12698,
          "@type": "TBD#LengthI",
          "Unit": "MICROMETER"
        },
        "PhysicalSizeZ": {
          "Symbol": "µm",
          "Value": 0.2,
          "@type": "TBD#LengthI",
          "Unit": "MICROMETER"
        },
        "Type": {
          "omero:details": {
            # omitted for brevity
          },
          "@id": 6,
          "@type": "TBD#PixelsType",
          "value": "uint16"
        },
        "omero:sha1": "eae01c54191fd9cf4b09e3651e1899d677375b7d",
        "omero:details": {
          # omitted for brevity
        },
        "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Pixels",
        "SignificantBits": 16
      },
      "omero:series": 0,
      "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Image"
    }
  ]
}

Images in a Dataset

Images can be filtered by parent Dataset using the ?dataset=id query string but you can also show Images in a Dataset using this URL:

GET     /api/v0/m/datasets/{dataset_id}/images/

Get a single Image

GET   /api/v0/m/images/{image_id}/

Response

The response for a single Image is the same as for listing Images above with the addition of Channels data.

{
  "data": [
    {
      "@id": 16783,
      "Name": "CFP_AurB_R3D.dv",
      "AcquisitionDate": 1235730332000,
      "omero:details": {
        # omitted for brevity
      },
      "Pixels": {
        "@id": 12801,
        "Channels": [
          {
            "omero:photometricInterpretation": {
              "omero:details": {},
              "@id": 5,
              "@type": "TBD#PhotometricInterpretation",
              "value": "Monochrome"
            },
            "Name": "CFP_JP4",
            "Color": 65535,
            "omero:details": {},
            "ExcitationWavelength": {
              "Symbol": "nm",
              "Value": 436,
              "@type": "TBD#LengthI",
              "Unit": "NANOMETER"
            },
            "SamplesPerPixel": 1,
            "NDFilter": 1,
            "EmissionWavelength": {
              "Symbol": "nm",
              "Value": 470,
              "@type": "TBD#LengthI",
              "Unit": "NANOMETER"
            },
            "omero:LogicalChannelId": 12301,
            "@id": 14451,
            "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Channel"
          },
          {
            "omero:photometricInterpretation": {
              "omero:details": {},
              "@id": 5,
              "@type": "TBD#PhotometricInterpretation",
              "value": "Monochrome"
            },
            "Name": "RD_TR-PE",
            "Color": -16776961,
            "omero:details": {},
            "ExcitationWavelength": {
              "Symbol": "nm",
              "Value": 555,
              "@type": "TBD#LengthI",
              "Unit": "NANOMETER"
            },
            "SamplesPerPixel": 1,
            "NDFilter": 0,
            "EmissionWavelength": {
              "Symbol": "nm",
              "Value": 617,
              "@type": "TBD#LengthI",
              "Unit": "NANOMETER"
            },
            "omero:LogicalChannelId": 12303,
            "@id": 14453,
            "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Channel"
          }
        ],
        "SizeX": 512,
        "SizeY": 512,
        "SizeZ": 29,
        "SizeC": 2,
        "SizeT": 1,
        "PhysicalSizeX": {
          "Symbol": "µm",
          "Value": 0.12698,
          "@type": "TBD#LengthI",
          "Unit": "MICROMETER"
        },
        "PhysicalSizeY": {
          "Symbol": "µm",
          "Value": 0.12698,
          "@type": "TBD#LengthI",
          "Unit": "MICROMETER"
        },
        "PhysicalSizeZ": {
          "Symbol": "µm",
          "Value": 0.2,
          "@type": "TBD#LengthI",
          "Unit": "MICROMETER"
        },
        "Type": {
          "omero:details": {
            # omitted for brevity
          },
          "@id": 6,
          "@type": "TBD#PixelsType",
          "value": "uint16"
        },
        "omero:sha1": "eae01c54191fd9cf4b09e3651e1899d677375b7d",
        "omero:details": {
          # omitted for brevity
        },
        "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Pixels",
        "SignificantBits": 16
      },
      "omero:series": 0,
      "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Image"
    }
  ]
}

Screens, Plates and Wells

For more information on the Screen, Plate, Well data model, please see the documentation page.

List Screens

Parameters

Name        Type        Description
------------------------------------------------------------------
plate       Number      Filter Datasets by child Plate ID

These query parameters are also supported (see above):

offset, limit, owner, group, childCount, normalize

GET     /api/v0/m/screens/

Response

{
  "data": [
    {
      "@id": 582,
      "Name": "Test data",
      "Description": "This is the Screen description",
      "url:screen": "http://server.openmicroscopy.org/api/v0/m/screen/582/",
      "url:plates": "http://server.openmicroscopy.org/api/v0/m/screen/582/plates/",
      "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Screen",
      "omero:details": {
        # omitted for brevity
      }
    }
  ]
}

Get a single Screen

GET   /api/v0/m/screens/{screen_id}/

Response

{
  "data": {
    "@id": 582,
    "Name": "Test data",
    "Description": "This is the Screen description",
    "url:plates": "http://server.openmicroscopy.org/api/v0/m/screen/582/plates/",
    "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Screen",
    "omero:details": {
      # omitted for brevity
    }
  }
}

List Plates

Parameters

Name        Type        Description
------------------------------------------------------------------
screen      Number      Filter Plates by parent Screen ID

well        Number      Filter Plates by child Well ID

orphaned    Boolean     Find Plates that are not in any Screen

These query parameters are also supported (see above):

offset, limit, owner, group, childCount, normalize

GET     /api/v0/m/plates/

Response

{
  "data": [
    {
      "@id": 5067,
      "Name": "Plate name",
      "Rows": 8,
      "Columns": 12,
      "RowNamingConvention": "letter",
      "ColumnNamingConvention": "number",
      "ExternalIdentifier": "003857",
      "url:plate": "http://server.openmicroscopy.org/api/v0/m/plates/5067/",
      "url:plateacquisitions": "http://server.openmicroscopy.org/api/v0/m/plates/5067/plateacquisitions/",
      "url:wells": "http://server.openmicroscopy.org/api/v0/m/plates/5067/wells/",
      "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Plate",
      "omero:details": {
        # omitted for brevity
      }
    },
  ]
}

Plates in a Screen

Plates can be filtered by parent Screen using the ?screen=id query string but you can also show Plates in a Screen using this URL:

GET     /api/v0/m/screens/{screen_id}/plates/

Get a single Plate

GET   /api/v0/m/plates/{plate_id}/

Response

The response for a single Plate includes information on the WellSamples (fields) for each Well such as the min/max WellSampleIndex for the Plate.

{
  "data": {
    "@id": 5067,
    "Name": "Plate name",
    "Rows": 8,
    "Columns": 12,
    "RowNamingConvention": "letter",
    "ColumnNamingConvention": "number",
    "ExternalIdentifier": "003857",
    "url:plate": "http://server.openmicroscopy.org/api/v0/m/plates/5067/",
    "url:plateacquisitions": "http://server.openmicroscopy.org/api/v0/m/plates/5067/plateacquisitions/",
    "url:wells": "http://server.openmicroscopy.org/api/v0/m/plates/5067/wells/",
    "url:wellsampleindex_wells": [
      "http://server.openmicroscopy.org/api/v0/m/plates/5068/wellsampleindex/0/wells/",
      "http://server.openmicroscopy.org/api/v0/m/plates/5068/wellsampleindex/1/wells/",
      "http://server.openmicroscopy.org/api/v0/m/plates/5068/wellsampleindex/2/wells/",
      "http://server.openmicroscopy.org/api/v0/m/plates/5068/wellsampleindex/3/wells/"
    ],
    "omero:wellsampleIndex": [
      0,
      3
    ],
    "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Plate",
    "omero:details": {
      # omitted for brevity
    }
  }
}

List Plate Acquisitions

A Plate Acquisition (run) is a collection of WellSamples, grouped by an acquisition time. A Plate may contain zero, one or more Plate Acquisitions.

GET   /api/v0/m/plates/{plate_id}/plateacquisitions/

Response

{
  "data": [
    {
      "@id": 4217,
      "url:wellsampleindex_wells": [
        "http://server.openmicroscopy.org/api/v0/m/plateacquisitions/4217/wellsampleindex/0/wells/"
        "http://server.openmicroscopy.org/api/v0/m/plateacquisitions/4217/wellsampleindex/1/wells/"
        "http://server.openmicroscopy.org/api/v0/m/plateacquisitions/4217/wellsampleindex/2/wells/"
      ],
      "omero:details": {
        # omitted for brevity
      },
      "MaximumFieldCount": 3,
      "url:plateacquisition": "http://server.openmicroscopy.org/api/v0/m/plateacquisitions/4217/",
      "omero:wellsampleIndex": [
        0,
        2
      ],
      "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#PlateAcquisition"
    }
  ]
}

List Wells in a Plate

Each Well in a Plate may contain zero, one or many WellSamples (fields). By default, when listing Wells in a Plate, all of the WellSamples and Images will be loaded for each Well. Wells are ordered by Column and Row.

Parameters

The following query parameters can be used (as described above)

offset, limit, owner, normalize

GET   /api/v0/m/plates/{plate_id}/wells/

Note

If there are a large number of WellSamples per Well, this has the potential to load a large amount of data. This can be reduced by using a smaller limit on the number of Wells loaded or only loading a single WellSample per Well, as described below.

Response

{
  "data": [
    {
      "@id": 139,
      "Column": 0,
      "Row": 0,
      "omero:details": {
        # omitted for brevity
      },
      "url:well": "http://server.openmicroscopy.org/api/v0/m/wells/139/",
      "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Well",
      "WellSamples": [
        {
          "PositionX": {
            "Symbol": "reference frame",
            "Value": 21864.47,
            "@type": "TBD#LengthI",
            "Unit": "REFERENCEFRAME"
          },
          "PositionY": {
            "Symbol": "reference frame",
            "Value": 36711.98,
            "@type": "TBD#LengthI",
            "Unit": "REFERENCEFRAME"
          },
          "omero:details": {
            # omitted for brevity
          },
          "Image": {
            "Name": "plate1.HTD [Well E02 Field #1]",
            "AcquisitionDate": 1252939626000,
            "omero:details": {
              # omitted for brevity
            },
            "url:image": "http://server.openmicroscopy.org/api/v0/m/images/2942/",
            "omero:series": 120,
            "@id": 2942,
            "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Image",
            "Description": "Scan Time: Mon Sep 14 11:36:58 2009"
          },
          "PlateAcquisition": {
            "omero:details": {
              # omitted for brevity
            },
            "MaximumFieldCount": 4,
            "StartTime": 1252938959000,
            "EndTime": 1252939813000,
            "@id": 102,
            "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#PlateAcquisition"
          },
          "@id": 203,
          "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#WellSample"
        }
      ]
    }
  ]
}

It is also possible to list all Wells without filtering by Plate, using the top-level URL /api/v0/m/wells/ optionally filtering by the plate query parameter.

List Wells by WellSample Index

To list Wells in a Plate, loading only a single WellSample and Image per Well, you can filter by WellSample Index. This list of Wells will not include empty Wells (Wells that have no WellSamples and Images).

GET   /api/v0/m/plates/{plate_id}/wellsampleindex/{index}/wells/

It is also possible to use the Plate Acquisition ID instead of Plate ID, when the WellSample (field) at the specified index was acquired as part of that Plate Acquisition:

GET   /api/v0/m/plateacquisitions/{plateacquisition_id}/wellsampleindex/{index}/wells/

Get a single Well

When a single Well is loaded, this will include all the WellSamples and Images with Pixels loaded.

GET   /api/v0/m/wells/{well_id}/

ROIs and Shapes

Support for listing ROIs was added in API version 0.1. ROIs are linked to Images and contain one or more Shapes. Types of shape are Rectangle, Ellipse, Point, Line, Polyline, Polygon and Label. The Mask type is not currently supported by omero-marshal.

List ROIs

When ROIs are listed, their child Shapes will also be loaded.

Parameters

Name        Type        Description
------------------------------------------------------------------
image       Number      Filter ROIs by Image ID

These query parameters are also supported (see above):

offset, limit, owner, group, normalize

GET     /api/v0/m/rois/

Response

{
  "data": [
    {
      "@id": 454,
      "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ROI",
      "shapes": [
        {
          "FontStyle": "Normal",
          "Locked": false,
          "Width": 98,
          "omero:details": {
            # omitted for brevity
          },
          "Height": 135,
          "FontFamily": "sans-serif",
          "StrokeWidth": {},
          "FontSize": {
            "Symbol": "pt",
            "Value": 12,
            "@type": "TBD#LengthI",
            "Unit": "POINT"
          },
          "FillColor": 1073741824,
          "Y": 192,
          "X": 189,
          "StrokeColor": -993737532,
          "TheT": 23,
          "@id": 713,
          "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Rectangle",
          "TheZ": 1
        }
      ],
      "omero:details": {
        # omitted for brevity
      },
    },
  ]
}

ROIs on an Image

ROIs can be filtered by Image using the ?image=id query string but you can also show ROIs on an Image using this URL:

GET     /api/v0/m/images/{image_id}/rois/

Creating and saving objects

The JSON API currently supports creating and saving of a limited number of object types, namely Projects, Datasets and Screens. It is not yet possible to save objects with unloaded objects, such as an Image without Pixels or Channels loaded. We will be working to resolve these issues in future releases.

Creating and saving of JSON objects are handled by a single save URL and objects are identified by their @type and @id attributes.

Object types

The object @type must be based on the currently supported Schema URL which can be retrieved with:

GET     /api/v0/

Response

{
  "url:schema": "http://www.openmicroscopy.org/Schemas/OME/2016-06",
  # other urls not shown
}

This can then be used to create a @type by appending # and the object name, such as:

http://www.openmicroscopy.org/Schemas/OME/2016-06#Project

Creating objects

To create an object, POST the JSON for that object, including the ID of the OMERO group that the object should be saved in. Currently only creation of Projects, Datasets and Screens is supported.

POST  /api/v0/m/save/?group={group_id}

Content

{
  "Name": "My new Project",
  "Description": "Created via the JSON API",
  "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project"
}

Response

{
  "data": {
    "@id": 567,
    "Name": "My new Project",
    "Description": "Created via the JSON API",
    "url:datasets": "http://server.openmicroscopy.org/api/v0/m/projects/3872/datasets/",
    "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project",
    "omero:details": {
      # omitted for brevity
    }
  }
}

Updating objects

The API supports PUT to replace existing objects with the submitted data. As mentioned above, the only objects that you can currently update are Projects, Datasets and Screens. The submitted JSON data can be constructed from scratch, but it will generally be more convenient and safer to GET the object, update it and save the edited JSON.

For example, to edit the Name of the Project in the previous example:

PUT   /api/v0/m/save/

Content

{
  "@id": 567,
  "Name": "Edited Project Name",
  "Description": "Created via the JSON API",
  "url:datasets": "http://server.openmicroscopy.org/api/v0/m/projects/3872/datasets/",
  "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project",
  "omero:details": {
    # omitted for brevity
  }
}

Response

{
  "data": {
    "@id": 567,
    "Name": "Edited Project Name",
    "Description": "Created via the JSON API",
    "url:datasets": "http://server.openmicroscopy.org/api/v0/m/projects/3872/datasets/",
    "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project",
    "omero:details": {
      # omitted for brevity
    }
  }
}

Deleting objects

To delete a Project, Dataset or Screen, simply DELETE using the URL to that object. The deleted object will be returned. For example, to delete a Project:

DELETE  /api/v0/m/projects/{project_id}/

Response

{
  "data": {
    "@id": 567,
    "Name": "Edited Project Name",
    "Description": "Created via the JSON API",
    "url:datasets": "http://server.openmicroscopy.org/api/v0/m/projects/3872/datasets/",
    "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project",
    "omero:details": {
      # omitted for brevity
    }
  }
}