# LIS integration

{% hint style="info" %}
LIS configuration is available on the Standard and Enterprise plans 
{% endhint %}

Go to the [**LIS page**](https://app.celly.ai/lis/). If LIS Integration is activated, your LIS can make requests to the Celly server and get analysis results.

{% hint style="success" %}
Use [basic authentication](https://en.wikipedia.org/wiki/Basic_access_authentication) for all requests with **Organization ID** as login and **Secret key** as password. **Organization ID** and **Secret key** can be found at <https://app.celly.ai/lis/>
{% endhint %}

<figure><img src="https://357738419-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-MJNQBgYLwFTXBIbt1TJ%2Fuploads%2FaUvqDkJTNGFx6zTFT4xe%2F%D0%A1%D0%BD%D0%B8%D0%BC%D0%BE%D0%BA%20%D1%8D%D0%BA%D1%80%D0%B0%D0%BD%D0%B0%202023-02-26%20%D0%B2%2012.29.03.png?alt=media&#x26;token=da92f946-15a8-4753-8c89-966b056d417f" alt=""><figcaption><p>Find your organization ID and Secret Key on the <a href="https://app.celly.ai/lis/">LIS page</a> </p></figcaption></figure>

Celly provides APIs that return analysis results to LIS:

1. <https://app.celly.ai/api/lis/v1/analysis/kinds> - returns a list of id and corresponding analysis types

   * `curl -X GET "https://app.celly.ai/api/lis/v1/analysis/kinds" -H "accept: application/json" -H "authorization: Basic $credentials$"`

   ```
   [
     {
       "id": 0,
       "name": "Blood: CBC"
     },
     {
       "id": 1,
       "name": "Bone marrow: WBC-differential"
     },
     {
       "id": 2,
       "name": "Malaria thin: parasites detection"
     },
     {
       "id": 3,
       "name": "Malaria thin: parasites counting"
     },
     {
       "id": 4,
       "name": "Slide Scan"
     },
     {
       "id": 5,
       "name": "Malaria thick: parasites counting"
     },
     {
       "id": 6,
       "name": "Blood: PLT counting (Fonio)"
     },
     {
       "id": 7,
       "name": "Canine Blood: CBC"
     },
     {
       "id": 8,
       "name": "Feline Blood: CBC"
     },
     {
       "id": 9,
       "name": "Canine Blood: CBC, 40x"
     },
     {
       "id": 10,
       "name": "Blood: CBC, 40x"
     },
     {
       "id": 11,
       "name": "Feline Blood: CBC, 40x"
     },
     {
       "id": 14,
       "name": "Pap (liquid-based), 40x"
     },
     {
       "id": 12,
       "name": "Canine Reticulocytes, 100x"
     },
     {
       "id": 13,
       "name": "Feline Reticulocytes, 100x"
     }
   ]
   ```
2. <https://app.celly.ai/api/lis/v1/analysis/statuses> - returns a list of id and corresponding analysis statuses

   * `curl -X GET "https://app.celly.ai/api/lis/v1/analysis/statuses" -H "accept: application/json" -H "authorization: Basic $credentials$"`

   ```
   [
     {
       "id": 6,
       "name": "Pending"
     },
     {
       "id": 0,
       "name": "Active"
     },
     {
       "id": 1,
       "name": "Post Processing"
     },
     {
       "id": 2,
       "name": "In Review"
     },
     {
       "id": 3,
       "name": "Approved"
     },
     {
       "id": 4,
       "name": "Rejected"
     },
     {
       "id": 5,
       "name": "Error"
     }
   ]
   ```
3. <https://app.celly.ai/api/lis/v1/analysis> - provides a list of all tests (in **In Review** / **Approved** / **Rejected** status) of your organization

   * `curl -X GET "https://app.celly.ai/api/lis/v1/analysis?page=1&page_size=3" -H "accept: application/json" -H "authorization: Basic $credentials$"`
   * To list the tests that have not yet been submitted to LIS use `sent_to_lis=False`
   * To filter by status and kind use `kind=id` and `status=id` respectively
   * Use `page_size` to customize the page size, default is 20
   * Use `page` to navigate between pages
   * `count` - total number of filtered tests, `previous`/`next` - link to get previous/next page

   ```
   {
     "count": 107,
     "next": "http://app.celly.ai/api/lis/v1/analysis?page=2&page_size=3",
     "previous": null,
     "results": [
       {
         "test_id": 16914,
         "description": "94111395",
         "kind": {
           "id": 0,
           "name": "Blood: CBC"
         },
         "status": {
           "id": 2,
           "name": "In Review"
         },
         "sent_to_lis": false,
         "started_at": "2021-12-27T13:03:38.718838+03:00",
         "duration_sec": 632
       },
       {
         "test_id": 16913,
         "description": "9919268438",
         "kind": {
           "id": 0,
           "name": "Blood: CBC"
         },
         "status": {
           "id": 2,
           "name": "In Review"
         },
         "sent_to_lis": false,
         "started_at": "2021-12-27T12:58:24.264011+03:00",
         "duration_sec": 190
       },
       {
         "test_id": 16912,
         "description": "9919266523",
         "kind": {
           "id": 0,
           "name": "Blood: CBC"
         },
         "status": {
           "id": 2,
           "name": "In Review"
         },
         "sent_to_lis": false,
         "started_at": "2021-12-27T12:38:38.224161+03:00",
         "duration_sec": 200
       }
     ]
   }
   ```
4. [https://app.celly.ai/api/lis/v1/analysis/{test\_id}](https://app.celly.ai/api/lis/v1/analysis/%7Btest_id%7D) - provides results for the given test\_id&#x20;
   * GET: returns results (format is described below)&#x20;
   * PATCH: returns results + marks the test as submitted to LIS (`sent_to_lis=True`)

Analysis result format:

```
"test_id" – unique test id in the Celly.AI database
"sent_to_lis" - is test marked as submitted to LIS? (bool)
"created_at" – created date (string)
"finished_at" – finished date(string)
"description" –  test description. Slide id from LIS will be here (string)
"conclusion" – conclusion text (string)
"kind_id" –  test type id
"status_id" - test status id
"user" –  user that performed the test (string)
"flags" –  report flags (json)
"snapshots"  - snapshot urls (array of strings)
"cell_counts" – cells number and images (json)
"tiles" - array of slide scan tiles (json) 
```

Result example (CBC test)

```
{
   "test_id":16914,
   "lis_id":null,
   "sent_to_lis":false,
   "created_at":"2021-12-27 10:03:38.448056+00:00",
   "finished_at":"2021-12-27 10:14:10.965686+00:00",
   "description":"94111395",
   "conclusion":null,
   "kind_id":0,
   "status_id":2,
   "user":"Dialab",
   "snapshots":[
      "https://cdn.celly.ai/website/media/app/...",
      ...
   ],
   "marked_cells":[
    { 
        "name": "Monocyte", 
        "comment": "check the cell", 
        "url": "https://cdn.celly.ai/website/media/app/..." 
    }, 
    ...
    ], 
    "tiles":[
       "https://cdn.celly.ai/website/panorama/deepzoom/0/0_0.jpg...",
       "https://cdn.celly.ai/website/panorama/deepzoom/1/0_1.jpg...",
       ...
       ],
   "cell_counts":{
      "backend":[
         {
            "name":"Segmented Neutrophil",
            "count":63,
            "ratio":70,
            "images":[
               "https://cdn.celly.ai/website/media/app/...",
               ...
            ]
         },
         ...
         {
            "name":"Total",
            "count":90,
            "ratio":100
         },
         {
            "name":"Unclassified",
            "count":8
         }
      ],
      "rbc_size":[
         {
            "name":"Normocytosis",
            "count":294,
            "ratio":98,
            "images":[
               "https://cdn.celly.ai/website/media/app/...",
               ...
            ]
         },
         ...
         {
            "name":"Total",
            "count":300,
            "ratio":100
         }
      ],
      "rbc_color":[
         {
            "name":"Normochromia",
            "count":300,
            "ratio":100,
            "images":[
               "https://cdn.celly.ai/website/media/app/...",
               ...
            ]
         },
         ...
         {
            "name":"Total",
            "count":300,
            "ratio":100
         }
      ],
      "rbc_shape":[
         {
            "name":"Normal",
            "count":288,
            "ratio":100,
            "images":[
               "https://cdn.celly.ai/website/media/app/...",
               ...
            ]
         },
         ...
         {
            "name":"Total",
            "count":288,
            "ratio":100
         },
         {
            "name":"Unclassified",
            "count":12
         }
      ],
      "rbc_inc":[
         {
            "name":"Parasites",
            "count":215,
            "ratio":71.7,
            "images":[
               "https://cdn.celly.ai/website/media/app/...",
               ...
            ]
         },
         ...
         {
            "name":"Total",
            "count":300,
            "ratio":100
         }
      ]
   },
   "flags":{
      "wbc":{
         "Megaloblasts":0,
         "Neutrophil hypersegmentation":0,
         "Toxic granulation of neutrophils":0,
         "Erythro, normoblasts":0
      },
      "plt":{
         "Giant PLT":0,
         "Clumps":0
      },
      "rbc":{
         "Anisocytosis":0,
         "Microcytosis":0,
         "Macrocytosis":0,
         "Anisochromia":0,
         "Hypochromia":0,
         "Hyperchromia":0,
         "Poikilocytosis":0,
         "Kodocytes":0,
         "Schizocytes":0,
         "Spherocytes":0,
         "Ovalocytes":0,
         "Teardrop":0,
         "Stomatocytes":0,
         "Acanthocytes":0,
         "Echinocytes":0,
         "Drepanocytes":0,
         "Parasites":0,
         "Cabot rings":0,
         "Howell-Jolly bodies":0,
         "Pappenheimer bodies":0,
         "Basophilic stippling":0
      }
   }
}
```

You can try the API out at Swagger documentation page <https://app.celly.ai/docs/lis>