Datature Nexus supports three annotation formats for 3D medical imaging projects:

• One-Hot Segmentation for NIfTI files
• Class-Index Segmentation for NIfTI files
• DICOM RT Structure Sets for DICOM files

❗️

Please note that uploading an annotation that already exists in the platform will result in overlapping annotations.

NIfTI

📘

Note:

Import all files in .nii or .nii.gz, .json formats respectively.

One-Hot Segmentation

Format Preview

.nii, .nii.gz

[
    // Channel 0 (class 1)
    [[[1, 1, 0, 0],
      [1, 0, 0, 1],
      [0, 0, 1, 1]],
     
     [[1, 0, 0, 1],
      [0, 0, 0, 1],
      [0, 0, 1, 1]]],

    // Channel 1 (class 2)
    [[[0, 0, 1, 1],
      [0, 1, 1, 0],
      [0, 0, 0, 0]],
     
     [[0, 1, 1, 0],
      [0, 0, 1, 0],
      [0, 0, 0, 0]]]
]  // Each channel contains binary masks (0 or 1)

labels.json

[
    {
        "id": 1,
        "name": "class1"
    },
    {
        "id": 2,
        "name": "class2"
    }
]

Class-Index Segmentation

Format Preview

.nii, .nii.gz

[
    [[0, 0, 1, 1],
     [0, 1, 1, 0],
     [2, 2, 0, 0]],
    
    [[0, 1, 1, 0],
     [2, 2, 1, 0],
     [2, 2, 0, 0]]
]

labels.json

[
    {
        "id": 1,
        "name": "class1"
    },
    {
        "id": 2,
        "name": "class2"
    }
]

DICOM

📘

Note:

Import all files in .dcm format.

DICOM RT Structure Set

Format Preview

DICOM RT Structure Sets define regions of interest (ROIs) within 3D medical image series using contour data. When importing RT Structure Set files (.dcm), each file must reference exactly one DICOM study. For each ROI in an RT Structure Set file, the system renders a 3D bitmask derived from the associated contour data, imports this bitmask as a new annotation for the corresponding DICOM 3D image series asset, and applies the ROI name as the tag name.

Supported Contour Geometric Types (3006, 0042)

• POINT: A single coordinate point.
• OPEN_PLANAR: An open contour with coplanar points.
• CLOSED_PLANAR: A polygon composed of coplanar points.
• CLOSEDPLANAR_XOR: Multiple coplanar polygons combined using XOR operations.

📘

Note:

The OPEN_NON_PLANAR type is not currently supported.

.dcm

DICOM File Meta -------------------------------------------------------
...
(0002, 0002) Media Storage SOP Class UID            UI: RT Structure Set Storage
...

DICOM Data Set --------------------------------------------------------
...
(0008, 0016) SOP Class UID                          UI: RT Structure Set Storage
...
# Must match the Study Instance UID of a 3D DICOM series uploaded or synced
# to the project as an asset.
(0020, 000D) Study Instance UID                     UI: ...
...
(3006, 0020) Structure Set ROI Sequence             ... item(s) ------
  (3006, 0022) ROI Number                           IS: '1'
  (3006, 0024) Referenced Frame Of Reference UID    UI: ...
  (3006, 0026) ROI Name                             LO: 'ROI 1'
  ...
  ------------
  ...
...
(3006, 0039) ROI Contour Sequence                   ... item(s) ------
  ...
  (3006, 0040) Contour Sequence                     ... item(s) ------
    (3006, 0016) Contour Image Sequence             ... item(s) ------
      # Defines images within the study containing the contour
      (0008, 1150) Referenced SOP Class UID         UI: ...
      (0008, 1155) Referenced SOP Instance UID
      ...
      ------------
      ...
    # Supported types are: POINT, OPEN_PLANAR, CLOSED_PLANAR, CLOSEDPLANAR_XOR.
    (3006, 0042) Contour Geometric Type             CS: 'CLOSED_PLANAR'
    (3006, 0046) Number of Contour Points           IS: '330'
    ...
    # Flattened sequence of (x, y, z) contour coordinates in patient-based
    # coordinate system.
    (3006, 0050) Contour Data                       DS: Array of 990 elements
    ------------
    ...
  ...
  (3006, 0084) Referenced ROI Number                IS: '1'
  ------------
  ...
...