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caMicroscope API Guide
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Resource
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HTTP VERB
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QueryEndpoint
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Query Parameters(Input)
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OutPut
(Description)
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Other Description
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/ImageLoader
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Node App that extracts image metadata and stores in mongo
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POST
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Naming
- case_id: Used to uniquely identify an image.
- execution_id: Used to uniquely identify an algorithm. A case_id can have multiple execution_ids associated with it.
- subject_id: Used to uniquely idenify a patient. A subject_id can have multiple case_ids associated with it.
/ImageLoader
The /ImageLoader resource is a Node application that extracts image metadata (such as width and height of the image) from the existing whole slide image and stores it in a Mongo database.
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/submitImage
HTTP Verb | QueryEndpoint | Query Parameters(Input) | Output(Description) |
|---|---|---|---|
| POST | /submitImage |
| case_id, File_location, subject_id | {“status”: “Success”} on success |
Example of /ImageLoader
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/uAIMDataLoader
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Node App that converts masks to GeoJSON and stores in Mongo
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POST
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| Code Block |
|---|
curl -v -F case_id=TCGA-02-0001 -F file_location=@TCGA-02-0001-01Z-00-DX1.83fce43e-42ac-4dcd-b156-2908e75f2e47.svs http://localhost:32799/submitData |
Optional study_id Return type: json On success returns: {"status":"success"}
case_id: The unique identifier for the image
file_location: Location of the image on file system
/uAIMDataLoader
Node application that converts Aperio and binary masks to GeoJSON objects and stores them in a Mongo database
HTTP Verb | QueryEndpoint | Query Parameters(Input) | Output(Description) |
|---|---|---|---|
POST | /submitMaskOrder |
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Case_id, Execution_id, Height, Width, X, Y, Type(optional) | {“jobId”: 12} | |
GET | /job/:id |
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GET
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/job/:id
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{“status”:”incomplete”}
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/ImageData
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Bindaas
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GET
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| None | {“status”:”incomplete”} |
Example of /uAIMDataLoader
Example cURL command (Aperio):
| Code Block |
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$ curl localhost:6000/submitMaskOrder -F mask=@1.png -F case_id=cbtc_test_11 -F execution_id=ganesh:test2 -F width=1743 -F height=2017 -F x=0 -F y=0 |
Example cURL command (binary mask):
| Code Block |
|---|
$ curl localhost:6000/submitMaskOrder -F mask=@1.xml -F case_id=cbtc_test_11 -F execution_id=ganesh:test2 -F width=1743 -F height=2017 -F x=0 -F y=0 -F type= maskfile |
| Variable | Definition |
|---|---|
| case_id | The unique identifier for the image |
| execution_id | The name(label) of the algorithm/run |
| width | width of the image/roi |
| height | height of the image/roi |
| x | top left x coordinate of the image/roi (Default: 0) |
| y | top left y coordinate of the image/roi (Default: 0) |
/ImageData
Bindaas APIs for handling Image Metadata. (Internal APIs, not meant to be exposed)
HTTP Verb | QueryEndpoint | Query Parameters(Input) | Output(Description) | Additional Description |
|---|---|---|---|---|
GET |
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/fileLocation | case_id |
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| Get file location of image | Used by the caMicroscope viewer to give the image location to its backend server. |
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| /mpp | case_id |
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Get mpp-x, mpp-y of the image | Used by the viewer to adjust the scales. |
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| /metadata | case_id |
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Get all metadata of the image(width, height, mpp etc.) | Used by dynamic services to get width, height, and file location of the image. |
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| /md5 | case_id |
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POST
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/json
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/MarkupData
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Bindaas
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GET
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/multipleMarkups
Get MD5 of the image file | Used to check the MD5 to make sure that the image was loaded successfully. | |||
| POST | /json | metdata | metadata of the image in JSON format | Stored in Mongo(db: Camicroscope, collection: ImageData). |
Example of /ImageData
POST
| Code Block |
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$ curl -H "Content-Type: application/json" -X POST -d '{"case_id": "TCGA-01-0001", "width": 30000, "height": 31000}' http://localhost:9099/Camicroscope/ImageData/json
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GET
| Code Block |
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$ curl http://localhost:9099/Camicroscope/ImageData/fileLocation
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/MarkupData
Bindaas
HTTP Verb | QueryEndpoint | Query Parameters(Input) | Output(Description) | Additional Information |
|---|---|---|---|---|
GET | /multipleMarkups | case |
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| _id, x1,y1,x2,y2,footprint,algorithms | GeoJSON |
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x1, y1, x2, y2 are the coordinates of a rectangular region of interest. (x1,y1) is the top-left coordinate pair. (x2, y2) is the bottom-right coordinate pair. |
| N/A |
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/executionIds | case_id | List of execution IDs available for a case | The case_id uniquely identifies an image. The execution_ids identify the image segmentation algorithm that is run on images. The results of these images appear as green polygons in caMicroscope. |
Examples of /MarkupData
/uAIMTemplates
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Bindaas
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GET
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/template
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id?
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Jsonform template
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Schema: https://github.com/joshfire/jsonform
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POST
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/json
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/Tasks
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Firebase/Kue???
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POST
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/task
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GET
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Schema: https://github.com/joshfire/jsonformMultiexcerpt include MultiExcerptName ExitDisclaimer nopanel true PageWithExcerpt wikicontent:Exit Disclaimer to Include
HTTP Verb | QueryEndpoint | Query Parameters(Input) | Output(Description) |
|---|---|---|---|
| GET | /template | N/A | Jsonform template |
POST | /json | Form in JSON format(see this) | 200 OK |
Examples of /uAIMTemplates
Examples of authoring a JSON form can be seen here.
Jobs
APIs for posting and retrieving tasks for caMicroscope. It uses Kue
to maintain the tasks. It is well documented.Multiexcerpt include MultiExcerptName ExitDisclaimer nopanel true PageWithExcerpt wikicontent:Exit Disclaimer to Include
HTTP Verb | QueryEndpoint | Query Parameters(Input) | Output(Description) |
|---|---|---|---|
POST | /job | Job data in JSON format | N/A |
| GET | task_id | N/A |
Examples of /Tasks
| Code Block | ||||
|---|---|---|---|---|
| ||||
$ curl -H "Content-Type: application/json" -X POST -d \
'{
"type": "order",
"data": {
},
"options" : {
"attempts": 5,
"priority": "high"
}
}' http://localhost:3000/job
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will output:
{"message": "job created", "id": 3}
This ID can be used to query the status of the job.
| Code Block | ||||
|---|---|---|---|---|
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curl http://localhost/job/3 |
| Code Block | ||||
|---|---|---|---|---|
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{"id":"3","type":"queue","data":{},"priority":-10,"progress":"100","state":"complete","attempts":null,"created_at":"1309973155248","updated_at":"1309973155248","duration":"15002"}
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/task
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task_id
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