LIS integration

Celly lets labs manage the data and store all the reports in their own LIS

LIS configuration is available on the Standard and Enterprise plans

Go to the LIS page. If LIS Integration is activated, your LIS can make requests to the Celly server and get analysis results.

Use basic 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/

Find your organization ID and Secret Key on the LIS page

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} - provides results for the given test_id

   • GET: returns results (format is described below)

   • 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