Volumes Annotation

Volume Project
Project Structure Example
Root folder for the project named project name
meta.json file
key_id_map.json file (optional)
Dataset folders, Each named dataset_name, which contains:
volume folder, contains source volume files in .nrrd file-format, for example volume1.nrrd
ann - folder, with annotations for volumes. (named as volume + .json) for example volume1.nrrd.json
volumetric_interpolation optional folder, created automatically while downloading project.
folders, named according to volume (volume1_nrrd), which contains an additional data files in STL file format, named with hex hash code of objects from key_id_map. For example: 24a56a26ed784e648d3dd6c5186b46ca.stl
Format of Annotations
For example (/project_name/dataset_name/ann/volume1.nrrd.json)
{
    "volumeId": 2388727,
    "volumeName": "volume1.nrrd",
    "datasetId": 42699,
    "volumeMeta": {
        "ACS": "RAS",
        "intensity": {"max": 3071, "min": -3024},
        "windowWidth": 6095,
        "rescaleSlope": 1,
        "windowCenter": 23.5,
        "channelsCount": 1,
        "dimensionsIJK": {"x": 512, "y": 512, "z": 139},
        "IJK2WorldMatrix": [
                            0.7617189884185793, 0,                  0,    -194.238403081894,
                            0,                  0.7617189884185793, 0,    -217.5384061336518,
                            0,                  0,                  2.5,  -347.7500000000001,
                            0,                  0,                  0,    1
                        ],
        "rescaleIntercept": 0
    },
    "createdAt": "2021-11-13T08:05:28.771Z",
    "updatedAt": "2021-11-13T08:05:28.771Z",
    "description": "",
    "tags": [],
    "objects": [
        {
            "id": 593494,
            "datasetId": 42699,
            "labelerLogin": "username",
            "createdAt": "2021-11-13T08:05:28.771Z",
            "updatedAt": "2021-11-13T08:05:28.771Z",
            "tags": [],
            "entityId": 2388727,
            "classTitle": "v"
        },
        {
            "id": 593495,
            "datasetId": 42699,
            "tags": [],
            "entityId": 2388727,
            "classTitle": "bbb"
        }
    ],
    "planes": [
        {
            "name": "axial",
            "normal": {
                "x": 0,
                "y": 0,
                "z": 1
            },
            "slices": [
                {
                    "index": 51,
                    "figures": [
                        {
                            "id": 57036532,
                            "objectId": 593494,
                            "description": "",
                            "geometryType": "bitmap",
                            "labelerLogin": "username",
                            "createdAt": "2021-11-13T08:05:28.771Z",
                            "updatedAt": "2021-11-13T08:05:28.771Z",
                            "geometry": {
                                "bitmap": {
                                    "data": "eJwBp ... AADUlIRFIAAACeA==",
                                    "origin": [
                                        156,
                                        275
                                    ]
                                }
                            }
                        }
                    ]
                },
                {
                    "index": 68,
                    "figures": [
                        {
                            "id": 57036538,
                            "objectId": 593495,
                            "description": "",
                            "geometryType": "rectangle",
                            "geometry": {
                                "points": {
                                    "exterior":[[305, 380], [167, 256]],
                                    "interior": []
                                }
                            }
                        }
                    ]
                }
​
            ]
        }
    ]
}
Fields definitions:
description - string - (optional) - this field is used to store the text we want to assign to the volume
tags - list of strings that will be interpreted as volume tags
objects - list of objects that may be present on the volume
planes - a list of figures that defined in these planes: coronal, sagittal, axial​
volumeMeta - meta data for 3D reconstruction of volume
labelerLogin - string - the name of the user that added this figure to the current frame
Fields definitions for objects field:
id - int, an unique identifier of given object (used in key_id_map.json to get the object KEY
classTitle - string - the title of a class. It's used to identify the class shape from the meta.json file
tags - list of strings that will be interpreted as object tags
labelerLogin - string - the name of the user that added this figure to the project
Fields description for volumeMeta field:
ACS - string - "RAS" or "LPS" - name of type of Anatomical coordinate system i.e. RAS means is Right-Anterior-Superior
╔════════╦════════════╗
║ Common ║ Anatomical ║
╠════════╬════════════╣
║ Left   ║ Left       ║
║ Right  ║ Right      ║
║ Up     ║ Superior   ║
║ Down   ║ Inferior   ║
║ Front  ║ Anterior   ║
║ Back   ║ Posterior  ║
╚════════╩════════════╝
intensity - {"min": int, "max": int} - intensity range. Depends on the device getting the data
windowWidth - float - Specify a linear conversion. Window Width contains the width of the window
windowCenter - float - Specify a linear conversion. Window Center contains the value that is the center of the window
channelsCount - float - channel count of your image data. Default: 1
dimensionsIJK - dict {"x": int, "y": int, "z": int} - dimensions of volume described as vector in IJK notation​
IJK2WorldMatrix - matrix to transform coordinates from IJK to world (cartesian). See here​
Grayscale transformations to be applied to Pixel Data are defined by the equivalent of the Modality LUT and Rescale Intercept, Value of Interest Attributes, Photometric Interpretation and the equivalent of the Presentation LUT.
units = m*SV + b
rescaleSlope - float - m in the equation specified by Rescale Intercept
rescaleIntercept - float - The value "b" in the relationship between stored values (SV) in Pixel Data and the output units specified in Rescale Type.
Fields description for planes field:
name - string - the name of the plane, where the figures are placed. Can be coronal, sagittal or axial 
​
normal - dict with x,y,z as a keys and 0/1 as a values - normal is direction by axis, chosen according to plane name
sagittal - x
coronal - y
axial - z
The value is binary (int 0 or 1) and one plane must be selected.
slices - list of slices on the plane. Each list contain index and may contain figures.
Fields description for slices field:
index - int value of slice index
figures - list of figures placed on slice. It can be bitmap or rectangle.
Key id map file
Key_id_map.json file is optional. It is created when annotating the episode inside Supervisely interface and sets the correspondence between the unique identifiers of the object and the frame on which the figure is located. If you annotate manually, you do not need to create this file. This will not affect the work being done.
Json format of key_id_map.json:
{
    "tags": {},
    "objects": {
        "198f727d40c749eebcacc4aed299b39a": 20520
    },
    "figures": {
        "65f21690780e43b49863c3cbd07eab3a": 503130811
    }
}

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Outline

Project Structure Example

Format of Annotations

Key id map file