The Public API from Aignostics — 21 operation(s) for public.
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openapi: 3.2.0
info:
title: Aignostics Platform Public API
description: The Aignostics Platform is a cloud-based service that enables organizations to access advanced computational pathology applications through a secure API.
version: 1.8.0
servers:
- url: /api
tags:
- name: Public
paths:
/v1/applications:
get:
tags:
- Public
summary: List available applications
description: 'Returns the list of the applications, available to the caller.
The application is available if any of the versions of the application is assigned to the caller''s organization.
The response is paginated and sorted according to the provided parameters.'
operationId: list_applications_v1_applications_get
security:
- OAuth2AuthorizationCodeBearer: []
parameters:
- name: page
in: query
required: false
schema:
type: integer
minimum: 1
default: 1
title: Page
- name: page-size
in: query
required: false
schema:
type: integer
maximum: 100
minimum: 5
default: 50
title: Page-Size
- name: sort
in: query
required: false
schema:
anyOf:
- type: array
items:
type: string
- type: 'null'
description: 'Sort the results by one or more fields. Use `+` for ascending and `-` for descending order.
**Available fields:**
- `application_id`
- `name`
- `description`
- `regulatory_classes`
**Examples:**
- `?sort=application_id` - Sort by application_id ascending
- `?sort=-name` - Sort by name descending
- `?sort=+description&sort=name` - Sort by description ascending, then name descending'
title: Sort
description: 'Sort the results by one or more fields. Use `+` for ascending and `-` for descending order.
**Available fields:**
- `application_id`
- `name`
- `description`
- `regulatory_classes`
**Examples:**
- `?sort=application_id` - Sort by application_id ascending
- `?sort=-name` - Sort by name descending
- `?sort=+description&sort=name` - Sort by description ascending, then name descending'
responses:
'200':
description: A list of applications available to the caller
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/ApplicationReadShortResponse'
title: Response List Applications V1 Applications Get
example:
- application_id: he-tme
name: Atlas H&E-TME
regulatory_classes:
- RUO
description: The Atlas H&E TME is an AI application designed to examine FFPE (formalin-fixed, paraffin-embedded) tissues stained with H&E (hematoxylin and eosin), delivering comprehensive insights into the tumor microenvironment.
latest_version:
number: 1.0.0
released_at: '2025-09-01T19:01:05.401Z'
- application_id: test-app
name: Test Application
regulatory_classes:
- RUO
description: 'This is the test application with two algorithms: TissueQc and Tissue Segmentation'
latest_version:
number: 2.0.0
released_at: '2025-09-02T19:01:05.401Z'
'401':
description: Unauthorized - Invalid or missing authentication
'422':
description: Validation Error
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
/v1/applications/{application_id}:
get:
tags:
- Public
summary: Read Application By Id
description: Retrieve details of a specific application by its ID.
operationId: read_application_by_id_v1_applications__application_id__get
security:
- OAuth2AuthorizationCodeBearer: []
parameters:
- name: application_id
in: path
required: true
schema:
type: string
title: Application Id
responses:
'200':
description: Successful Response
content:
application/json:
schema:
$ref: '#/components/schemas/ApplicationReadResponse'
'403':
description: Forbidden - You don't have permission to see this application
'404':
description: Not Found - Application with the given ID does not exist
'422':
description: Validation Error
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
/v1/applications/{application_id}/versions/{version}:
get:
tags:
- Public
summary: Application Version Details
description: 'Get the application version details.
Allows caller to retrieve information about application version based on provided application version ID.'
operationId: application_version_details_v1_applications__application_id__versions__version__get
security:
- OAuth2AuthorizationCodeBearer: []
parameters:
- name: application_id
in: path
required: true
schema:
type: string
title: Application Id
- name: version
in: path
required: true
schema:
type: string
pattern: ^(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)(?:-((?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\.(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\+([0-9a-zA-Z-]+(?:\.[0-9a-zA-Z-]+)*))?$
title: Version
responses:
'200':
description: Successful Response
content:
application/json:
schema:
$ref: '#/components/schemas/VersionReadResponse'
example:
version_number: 1.3.0
changelog: New deployment
input_artifacts:
- name: whole_slide_image
mime_type: image/tiff
metadata_schema:
type: object
title: Slide Schema
description: Schema of a slide.
$defs:
LungCancerSpecimen:
type: object
title: LungCancerSpecimen
required:
- disease
properties:
disease:
const: LUNG_CANCER
type: string
title: Disease
tissue:
enum:
- LUNG
- LYMPH_NODE
- LIVER
- ADRENAL_GLAND
- BONE
- BRAIN
- OTHER
type: string
title: Tissue
default: OTHER
additionalProperties: false
required:
- checksum_base64_crc32c
- staining_method
- specimen
properties:
checksum_base64_crc32c:
type: string
title: Base64 encoded big-endian CRC32C checksum
staining_method:
const: H&E
type: string
title: Staining Method
specimen:
anyOf:
- $ref: '#/$defs/LungCancerSpecimen'
title: Specimen
media_type:
anyOf:
- enum:
- application/dicom
- image/tiff
- application/octet-stream
- application/zip
type: string
- type: 'null'
title: Media Type
resolution_mpp:
anyOf:
- type: number
maximum: 0.55
minimum: 0.08
- type: 'null'
title: Resolution (mpp)
width_px:
anyOf:
- type: integer
minimum: 1
- type: 'null'
title: Width (px)
height_px:
anyOf:
- type: integer
minimum: 1
- type: 'null'
title: Height (px)
additionalProperties: false
output_artifacts:
- name: tissue_qc:segmentation_map_image
mime_type: image/tiff
metadata_schema:
type: object
title: SegmentationMapImageMetadata
description: Metadata corresponding to a segmentation map image.
required:
- checksum_base64_crc32c
- width_px
- height_px
- class_colors
properties:
checksum_base64_crc32c:
type: string
title: Base64 encoded big-endian CRC32C checksum
width_px:
type: integer
title: Width Px
height_px:
type: integer
title: Height Px
media_type:
const: image/tiff
type: string
title: Media Type
default: image/tiff
resolution_mpp:
type: number
title: Resolution Mpp
maximum: 0.55
minimum: 0.08
class_colors:
type: object
title: Class Colors
additionalProperties:
type: array
maxItems: 3
minItems: 3
prefixItems:
- type: integer
maximum: 255
minimum: 0
- type: integer
maximum: 255
minimum: 0
- type: integer
maximum: 255
minimum: 0
additionalProperties: false
scope: ITEM
visibility: EXTERNAL
released_at: '2025-04-16T08:45:20.655972Z'
'403':
description: Forbidden - You don't have permission to see this version
'404':
description: Not Found - Application version with given ID is not available to you or does not exist
'422':
description: Validation Error
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
/v1/runs:
get:
tags:
- Public
summary: List Runs
description: 'List runs with filtering, sorting, and pagination capabilities.
Returns paginated runs that were submitted by the user.'
operationId: list_runs_v1_runs_get
security:
- OAuth2AuthorizationCodeBearer: []
parameters:
- name: application_id
in: query
required: false
schema:
anyOf:
- type: string
- type: 'null'
description: Optional application ID filter
examples:
- tissue-segmentation
- heta
title: Application Id
description: Optional application ID filter
- name: application_version
in: query
required: false
schema:
anyOf:
- type: string
- type: 'null'
description: Optional Version Name
examples:
- 1.0.2
- 1.0.1-beta2
title: Application Version
description: Optional Version Name
- name: external_id
in: query
required: false
schema:
anyOf:
- type: string
- type: 'null'
description: Optionally filter runs by items with this external ID
examples:
- slide_001
- patient_12345_sample_A
title: External Id
description: Optionally filter runs by items with this external ID
- name: custom_metadata
in: query
required: false
schema:
anyOf:
- type: string
maxLength: 1000
- type: 'null'
description: "Use PostgreSQL JSONPath expressions to filter runs by their custom_metadata.\n#### URL Encoding Required\n**Important**: JSONPath expressions contain special characters that must be URL-encoded when used in query parameters. Most HTTP clients handle this automatically, but when constructing URLs manually, please ensure proper encoding.\n\n#### Examples (Clear Format):\n- **Field existence**: `$.study` - Runs that have a study field defined\n- **Exact value match**: `$.study ? (@ == \"high\")` - Runs with specific study value\n- **Numeric comparison**: `$.confidence_score ? (@ > 0.75)` - Runs with confidence score greater than 0.75\n- **Array operations**: `$.tags[*] ? (@ == \"draft\")` - Runs with tags array containing \"draft\"\n- **Complex conditions**: `$.resources ? (@.gpu_count > 2 && @.memory_gb >= 16)` - Runs with high resource requirements\n\n#### Examples (URL-Encoded Format):\n- **Field existence**: `%24.study`\n- **Exact value match**: `%24.study%20%3F%20(%40%20%3D%3D%20%22high%22)`\n- **Numeric comparison**: `%24.confidence_score%20%3F%20(%40%20%3E%200.75)`\n- **Array operations**: `%24.tags%5B*%5D%20%3F%20(%40%20%3D%3D%20%22draft%22)`\n- **Complex conditions**: `%24.resources%20%3F%20(%40.gpu_count%20%3E%202%20%26%26%20%40.memory_gb%20%3E%3D%2016)`\n\n#### Notes\n- JSONPath expressions are evaluated using PostgreSQL's `@?` operator\n- The `$.` prefix is automatically added to root-level field references if missing\n- String values in conditions must be enclosed in double quotes\n- Use `&&` for AND operations and `||` for OR operations\n- Regular expressions use `like_regex` with standard regex syntax\n- **Please remember to URL-encode the entire JSONPath expression when making HTTP requests**\n\n "
title: Custom Metadata
description: "Use PostgreSQL JSONPath expressions to filter runs by their custom_metadata.\n#### URL Encoding Required\n**Important**: JSONPath expressions contain special characters that must be URL-encoded when used in query parameters. Most HTTP clients handle this automatically, but when constructing URLs manually, please ensure proper encoding.\n\n#### Examples (Clear Format):\n- **Field existence**: `$.study` - Runs that have a study field defined\n- **Exact value match**: `$.study ? (@ == \"high\")` - Runs with specific study value\n- **Numeric comparison**: `$.confidence_score ? (@ > 0.75)` - Runs with confidence score greater than 0.75\n- **Array operations**: `$.tags[*] ? (@ == \"draft\")` - Runs with tags array containing \"draft\"\n- **Complex conditions**: `$.resources ? (@.gpu_count > 2 && @.memory_gb >= 16)` - Runs with high resource requirements\n\n#### Examples (URL-Encoded Format):\n- **Field existence**: `%24.study`\n- **Exact value match**: `%24.study%20%3F%20(%40%20%3D%3D%20%22high%22)`\n- **Numeric comparison**: `%24.confidence_score%20%3F%20(%40%20%3E%200.75)`\n- **Array operations**: `%24.tags%5B*%5D%20%3F%20(%40%20%3D%3D%20%22draft%22)`\n- **Complex conditions**: `%24.resources%20%3F%20(%40.gpu_count%20%3E%202%20%26%26%20%40.memory_gb%20%3E%3D%2016)`\n\n#### Notes\n- JSONPath expressions are evaluated using PostgreSQL's `@?` operator\n- The `$.` prefix is automatically added to root-level field references if missing\n- String values in conditions must be enclosed in double quotes\n- Use `&&` for AND operations and `||` for OR operations\n- Regular expressions use `like_regex` with standard regex syntax\n- **Please remember to URL-encode the entire JSONPath expression when making HTTP requests**\n\n "
examples:
no_filter:
summary: No filter (returns all)
description: Returns all items without filtering by custom metadata
value: $
field_exists:
summary: Check if field exists
description: Find applications that have a project field defined
value: $.study
field_has_value:
summary: Check if field has a certain value
description: Compare a field value against a certain value
value: $.study ? (@ == "abc-1")
numeric_comparisons:
summary: Compare to a numeric value of a field
description: Compare a field value against a numeric value of a field
value: $.confidence_score ? (@ > 0.75)
array_operations:
summary: Check if an array contains a certain value
description: Check if an array contains a certain value
value: $.tags[*] ? (@ == "draft")
complex_filters:
summary: Combine multiple checks
description: Combine multiple checks
value: $.resources ? (@.gpu_count > 2 && @.memory_gb >= 16)
- name: page
in: query
required: false
schema:
type: integer
minimum: 1
default: 1
title: Page
- name: page_size
in: query
required: false
schema:
type: integer
maximum: 100
minimum: 5
default: 50
title: Page Size
- name: submitted_by
in: query
required: false
schema:
anyOf:
- type: string
- type: 'null'
description: Filter runs by the user who submitted them. Use the special value `me` to return only runs submitted by the current user.
examples:
- me
- auth0|123456789
title: Submitted By
description: Filter runs by the user who submitted them. Use the special value `me` to return only runs submitted by the current user.
- name: organization_id
in: query
required: false
schema:
anyOf:
- type: string
- type: 'null'
description: Filter runs by the organization of the submitter. Use the special value `my_org` to filter by the current user's organization.
examples:
- my_org
- org_acme
title: Organization Id
description: Filter runs by the organization of the submitter. Use the special value `my_org` to filter by the current user's organization.
- name: for_organization
in: query
required: false
schema:
anyOf:
- type: string
- type: 'null'
description: Filter runs by organization ID. Available for superadmins (any org) and admins (own org only). When provided, returns all runs for the specified organization instead of only the caller's own runs.
title: For Organization
description: Filter runs by organization ID. Available for superadmins (any org) and admins (own org only). When provided, returns all runs for the specified organization instead of only the caller's own runs.
- name: sort
in: query
required: false
schema:
anyOf:
- type: array
items:
type: string
- type: 'null'
description: 'Sort the results by one or more fields. Use `+` for ascending and `-` for descending order.
**Available fields:**
- `run_id`
- `application_id`
- `version_number`
- `custom_metadata`
- `submitted_at`
- `submitted_by`
- `terminated_at`
- `termination_reason`
**Examples:**
- `?sort=submitted_at` - Sort by creation time (ascending)
- `?sort=-submitted_at` - Sort by creation time (descending)
- `?sort=state&sort=-submitted_at` - Sort by state, then by time (descending)
'
title: Sort
description: 'Sort the results by one or more fields. Use `+` for ascending and `-` for descending order.
**Available fields:**
- `run_id`
- `application_id`
- `version_number`
- `custom_metadata`
- `submitted_at`
- `submitted_by`
- `terminated_at`
- `termination_reason`
**Examples:**
- `?sort=submitted_at` - Sort by creation time (ascending)
- `?sort=-submitted_at` - Sort by creation time (descending)
- `?sort=state&sort=-submitted_at` - Sort by state, then by time (descending)
'
responses:
'200':
description: Successful Response
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/RunReadResponse'
title: Response List Runs V1 Runs Get
'404':
description: Run not found
'422':
description: Validation Error
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
post:
tags:
- Public
summary: Initiate Run
description: 'This endpoint initiates a processing run for a selected application and version, and returns a
`run_id` for tracking purposes.'
operationId: create_run_v1_runs_post
security:
- OAuth2AuthorizationCodeBearer: []
requestBody:
required: true
content:
application/json:
schema:
$ref: '#/components/schemas/RunCreationRequest'
responses:
'201':
description: Successful Response
content:
application/json:
schema:
$ref: '#/components/schemas/RunCreationResponse'
'404':
description: Application or application version not found
'400':
description: Bad Request - Input validation failed
'402':
description: Payment Required - A quota limit (slides per run, or monthly slides) would be exceeded by this run
'403':
description: Forbidden - You don't have permission to create this run
'422':
description: Validation Error
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
/v1/runs/{run_id}:
get:
tags:
- Public
summary: Get run details
description: 'This endpoint allows the caller to retrieve the current status of a run along with other relevant run details.
A run becomes available immediately after it is created through the `POST /v1/runs/` endpoint.
To download the output results, use `GET /v1/runs/{run_id}/` items to get outputs for all slides.
Access to a run is restricted to the user who created it, or users with an active grant or valid share token.'
operationId: get_run_v1_runs__run_id__get
security:
- OAuth2AuthorizationCodeBearer: []
parameters:
- name: run_id
in: path
required: true
schema:
type: string
format: uuid
description: Run id, returned by `POST /v1/runs/` endpoint
title: Run Id
description: Run id, returned by `POST /v1/runs/` endpoint
- name: share_token
in: query
required: false
schema:
anyOf:
- type: string
- type: 'null'
description: Share token for accessing shared runs
title: Share Token
description: Share token for accessing shared runs
responses:
'200':
description: Successful Response
content:
application/json:
schema:
$ref: '#/components/schemas/RunReadResponse'
'404':
description: Run not found because it was deleted.
'403':
description: Forbidden - You don't have permission to see this run
'422':
description: Validation Error
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
/v1/runs/{run_id}/cancel:
post:
tags:
- Public
summary: Cancel Run
description: 'The run can be canceled by the user who created the run.
The execution can be canceled any time while the run is not in the terminated state. The
pending items of a canceled run will not be processed and will not add to the cost.
When the run is canceled, the already completed items remain available for download.'
operationId: cancel_run_v1_runs__run_id__cancel_post
security:
- OAuth2AuthorizationCodeBearer: []
parameters:
- name: run_id
in: path
required: true
schema:
type: string
format: uuid
description: Run id, returned by `POST /runs/` endpoint
title: Run Id
description: Run id, returned by `POST /runs/` endpoint
responses:
'202':
description: Successful Response
content:
application/json:
schema: {}
'404':
description: Run not found
'403':
description: Forbidden - You don't have permission to cancel this run
'409':
description: Conflict - The Run is already cancelled
'422':
description: Validation Error
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
/v1/runs/{run_id}/items:
get:
tags:
- Public
summary: List Run Items
description: 'List items in a run with filtering, sorting, and pagination capabilities.
Returns paginated items within a specific run. Results can be filtered
by `item_id`, `external_ids`, `custom_metadata`, `terminated_at`, and `termination_reason` using JSONPath expressions.
## JSONPath Metadata Filtering
Use PostgreSQL JSONPath expressions to filter items using their custom_metadata.
### Examples:
- **Field existence**: `$.case_id` - Results that have a case_id field defined
- **Exact value match**: `$.priority ? (@ == "high")` - Results with high priority
- **Numeric comparison**: `$.confidence_score ? (@ > 0.95)` - Results with high confidence
- **Array operations**: `$.flags[*] ? (@ == "reviewed")` - Results flagged as reviewed
- **Complex conditions**: `$.metrics ? (@.accuracy > 0.9 && @.recall > 0.8)` - Results meeting performance thresholds
## Notes
- JSONPath expressions are evaluated using PostgreSQL''s `@?` operator
- The `$.` prefix is automatically added to root-level field references if missing
- String values in conditions must be enclosed in double quotes
- Use `&&` for AND operations and `||` for OR operations'
operationId: list_run_items_v1_runs__run_id__items_get
security:
- OAuth2AuthorizationCodeBearer: []
parameters:
- name: run_id
in: path
required: true
schema:
type: string
format: uuid
description: Run id, returned by `POST /v1/runs/` endpoint
title: Run Id
description: Run id, returned by `POST /v1/runs/` endpoint
- name: share_token
in: query
required: false
schema:
anyOf:
- type: string
- type: 'null'
description: Share token for accessing shared runs
title: Share Token
description: Share token for accessing shared runs
- name: item_id__in
in: query
required: false
schema:
anyOf:
- type: array
items:
type: string
format: uuid
- type: 'null'
description: Filter for item ids
title: Item Id In
description: Filter for item ids
- name: external_id__in
in: query
required: false
schema:
anyOf:
- type: array
items:
type: string
- type: 'null'
description: Filter for items by their external_id from the input payload
title: External Id In
description: Filter for items by their external_id from the input payload
- name: state
in: query
required: false
schema:
anyOf:
- $ref: '#/components/schemas/ItemState'
- type: 'null'
description: Filter items by their state
title: State
description: Filter items by their state
- name: termination_reason
in: query
required: false
schema:
anyOf:
- $ref: '#/components/schemas/ItemTerminationReason'
- type: 'null'
description: Filter items by their termination reason. Only applies to TERMINATED items.
title: Termination Reason
description: Filter items by their termination reason. Only applies to TERMINATED items.
- name: custom_metadata
in: query
required: false
schema:
anyOf:
- type: string
maxLength: 1000
- type: 'null'
description: JSONPath expression to filter items by their custom_metadata
title: Custom Metadata
description: JSONPath expression to filter items by their custom_metadata
examples:
no_filter:
summary: No filter (returns all)
description: Returns all items without filtering by custom metadata
value: $
field_exists:
summary: Check if field exists
description: Find items that have a project field defined
value: $.project
field_has_value:
summary: Check if field has a certain value
description: Compare a field value against a certain value
value: $.project ? (@ == "cancer-research")
numeric_comparisons:
summary: Compare to a numeric value of a field
description: Compare a field value against a numeric value of a field
value: $.duration_hours ? (@ < 2)
array_operations:
summary: Check if an array contains a certain value
description: Check if an array contains a certain value
value: $.tags[*] ? (@ == "production")
complex_filters:
summary: Combine multiple checks
description: Combine multiple checks
value: $.resources ? (@.gpu_count > 2 && @.memory_gb >= 16)
- name: page
in: query
required: false
schema:
type: integer
minimum: 1
default: 1
title: Page
- name: page_size
in: query
required: false
schema:
type: integer
maximum: 100
minimum: 5
default: 50
title: Page Size
- name: sort
in: query
required: false
schema:
anyOf:
- type: array
items:
type: string
- type: 'null'
description: "Sort the i
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