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 : 0.2
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.
Pagination
Requests that return a list of items will be paginated, showing
a limit of the first 200 objects by default.
Pagination can be specified using the limit and offset query
parameters:
# List the first 100 Projects (offset=0 by default)
<server>/api/v0/m/projects/?limit=100
# List the next 100 Projects
<server>/api/v0/m/projects/?limit=100&offset=100
Pagination details will be returned in a meta JSON object, including
the totalCount of objects for that query, the current offset and
limit as well as the maxLimit that you can use.
"meta": {
"totalCount": 13240,
"maxLimit": 500,
"limit": 200,
"offset": 0
},
Sysadmins can configure the default limit and maxLimit settings
for their server, for example:
$ omero config set omero.web.api.limit 100
$ omero config set omero.web.api.max_limit 300
The maxLimit setting prevents API consumers from requesting very
large amounts of data by limiting the number of top-level objects that
are loaded.
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=foowill 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
POSTto/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
messagereturned and check whether astacktraceis 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.
See the following link for a JSON client example https://github.com/ome/openmicroscopy/blob/develop/examples/Training/javascript/index.html.
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"
}
If you are using the API over HTTPS, you will also need to set the Referer key in
request headers when supplying the CSRF token to other endpoints. The referer URI
needs to be an address on the same domain as the server for the token to be accepted.
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": "https://server.openmicroscopy.org/api/v0/m/projects/11601/",
"url:datasets": "https://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": "https://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": "https://server.openmicroscopy.org/api/v0/m/dataset/112/",
"url:images": "https://server.openmicroscopy.org/api/v0/m/datasets/112/images/",
"url:projects": "https://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": "https://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": "https://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": "https://server.openmicroscopy.org/api/v0/m/screen/582/",
"url:plates": "https://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": "https://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": "https://server.openmicroscopy.org/api/v0/m/plates/5067/",
"url:plateacquisitions": "https://server.openmicroscopy.org/api/v0/m/plates/5067/plateacquisitions/",
"url:wells": "https://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": "https://server.openmicroscopy.org/api/v0/m/plates/5067/",
"url:plateacquisitions": "https://server.openmicroscopy.org/api/v0/m/plates/5067/plateacquisitions/",
"url:wells": "https://server.openmicroscopy.org/api/v0/m/plates/5067/wells/",
"url:wellsampleindex_wells": [
"https://server.openmicroscopy.org/api/v0/m/plates/5068/wellsampleindex/0/wells/",
"https://server.openmicroscopy.org/api/v0/m/plates/5068/wellsampleindex/1/wells/",
"https://server.openmicroscopy.org/api/v0/m/plates/5068/wellsampleindex/2/wells/",
"https://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": [
"https://server.openmicroscopy.org/api/v0/m/plateacquisitions/4217/wellsampleindex/0/wells/"
"https://server.openmicroscopy.org/api/v0/m/plateacquisitions/4217/wellsampleindex/1/wells/"
"https://server.openmicroscopy.org/api/v0/m/plateacquisitions/4217/wellsampleindex/2/wells/"
],
"omero:details": {
# omitted for brevity
},
"MaximumFieldCount": 3,
"url:plateacquisition": "https://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": "https://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": "https://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 Ellipse, Label, Line, Mask, Point, Polygon, Polyline and Rectangle.
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/
Experimenters and Groups
Support for listing Experimenters and Groups was added in API version 0.2. Experimenters are users of OMERO and can belong to one or more Groups. Groups are defined as ExperimenterGroups in the OME model.
Listing Experimenters
OMERO will only allow you to access details of Experimenters who are members of a non-private group that you are also a member of.
Parameters
Name Type Description
------------------------------------------------------------------
experimentergroup Number Filter Experimenters by Group
These query parameters are also supported (see above):
offset, limit
GET /api/v0/m/experimenters/
Response
{
"data": [
{
"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter",
"@id": 10,
"omero:details": {
"@type": "TBD#Details",
"permissions": {
"@type": "TBD#Permissions",
"perm": "------",
"canAnnotate": true,
"canDelete": false,
"canEdit": false,
"canLink": true,
"isWorldWrite": false,
"isWorldRead": false,
"isGroupWrite": false,
"isGroupRead": false,
"isGroupAnnotate": false,
"isUserWrite": false,
"isUserRead": false
}
},
"FirstName": "Ben",
"LastName": "Nevis",
"UserName": "ben",
"url:experimenter": "https://server.openmicroscopy.org/web/api/v0/m/experimenters/10/",
"url:experimentergroups": "https://server.openmicroscopy.org/web/api/v0/m/experimenters/10/experimentergroups/"
},
]
}
Get a single Experimenter
Load an Experimenter with:
GET /api/v0/m/experimenters/{experimenter_id}/
Experimenters in a Group
Experimenters can be filtered by Group using the ?experimentergroup=id query string but
you can also show Members of a Group using this URL:
GET /api/v0/m/experimentergroups/{group_id}/experimenters/
Listing Groups
Parameters
Name Type Description
------------------------------------------------------------------
experimenter Number Filter Groups by Experimenter
These query parameters are also supported (see above):
offset, limit
GET /api/v0/m/experimentergroups/
Response
{
"data": [
{
"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup",
"@id": 10,
"omero:details": {
"@type": "TBD#Details",
"permissions": {
"@type": "TBD#Permissions",
"perm": "------",
"canAnnotate": true,
"canDelete": false,
"canEdit": false,
"canLink": true,
"isWorldWrite": false,
"isWorldRead": false,
"isGroupWrite": false,
"isGroupRead": false,
"isGroupAnnotate": false,
"isUserWrite": false,
"isUserRead": false
}
},
"Name": "Swedlow Lab",
"url:experimentergroup": "https://server.openmicroscopy.org/web/api/v0/m/experimentergroups/10/",
"url:experimenters": "https://server.openmicroscopy.org/web/api/v0/m/experimentergroups/10/experimenters/"
},
]
}
Get a single Group
Load a Group with:
GET /api/v0/m/experimentergroups/{group_id}/
Groups for an Experimenter
Groups can be filtered by Experimenter using the ?experimenter=id query string but
you can also show ExperimenterGroups that an Experimenter belongs to using this URL:
GET /api/v0/m/experimenters/{experimenter_id}/experimentergroups
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": "https://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": "https://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": "https://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": "https://server.openmicroscopy.org/api/v0/m/projects/3872/datasets/",
"@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Project",
"omero:details": {
# omitted for brevity
}
}
}