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Segmentation Tools

In this tutorial, you will learn how to use the segmentation tools to draw and edit segmentations.

Preface​

In order to render a volume we need:

  • HTMLDivElements to render different orientation of the volume (e.g., one for Axial, one for Sagittal)
  • The path to the images (imageIds).

Implementation​

We have already stored images on a server for the purpose of this tutorial.

First let's create three HTMLDivElements and style them to contain viewports for Axial, Sagittal, and Coronal views.

const content = document.getElementById('content');

const viewportGrid = document.createElement('div');
viewportGrid.style.display = 'flex';
viewportGrid.style.flexDirection = 'row';

// element for axial view
const element1 = document.createElement('div');
element1.style.width = '500px';
element1.style.height = '500px';

// element for sagittal view
const element2 = document.createElement('div');
element2.style.width = '500px';
element2.style.height = '500px';

// element for coronal view
const element3 = document.createElement('div');
element3.style.width = '500px';
element3.style.height = '500px';

viewportGrid.appendChild(element1);
viewportGrid.appendChild(element2);
viewportGrid.appendChild(element3);

content.appendChild(viewportGrid);

For rendering Segmentations, add the SegmentationDisplayTool. This tool is used to render segmentations. For the brush tool, add the BrushTool. Both these tools should be added to the Cornerstone3D via the addTool API and the ToolGroup:

addTool(SegmentationDisplayTool);
addTool(BrushTool);

for the toolGroup:

const toolGroupId = 'CT_TOOLGROUP';
// Define tool groups to add the segmentation display tool to
const toolGroup = ToolGroupManager.createToolGroup(toolGroupId);

// Segmentation Tools
toolGroup.addTool(SegmentationDisplayTool.toolName);
toolGroup.addTool(BrushTool.toolName);

Next, in order for segmentations to be rendered, set the SegmentationDisplayTool to be enabled:

toolGroup.setToolEnabled(SegmentationDisplayTool.toolName);

And for having the brush tool active as the left mouse button is pressed, set the BrushTool to be active:

toolGroup.setToolActive(BrushTool.toolName, {
  bindings: [{ mouseButton: csToolsEnums.MouseBindings.Primary }],
});

Next, we can deal with volume loading. First, let's load the actual CT volume we are intending to use for rendering.

const volumeName = 'CT_VOLUME_ID';
const volumeLoaderScheme = 'cornerstoneStreamingImageVolume';
const volumeId = `${volumeLoaderScheme}:${volumeName}`;

// Define a volume in memory for CT
const volume = await volumeLoader.createAndCacheVolume(volumeId, {
  imageIds,
});

We need another volume for segmentation (we don't want to modify the CT volume for segmentation). We can use the CT volume (volumeId) as a reference for metadata to create a new volume for segmentation.

const segmentationId = 'MY_SEGMENTATION_ID';

// Create a segmentation of the same resolution as the source data for the CT volume
await volumeLoader.createAndCacheDerivedSegmentationVolume(volumeId, {
  volumeId: segmentationId,
});

Then, add the created segmentation to the Cornerstone3DTools segmentation state. This is done via the addSegmentation API:

// Add the segmentations to state. As seen the labelmap data
// which is the cached volumeId is provided to the state
segmentation.addSegmentations([
  {
    segmentationId,
    representation: {
      // The type of segmentation
      type: csToolsEnums.SegmentationRepresentations.Labelmap,
      // The actual segmentation data, in the case of labelmap this is a
      // reference to the source volume of the segmentation.
      data: {
        volumeId: segmentationId,
      },
    },
  },
]);
Important

Creation and addition of a segmentation to the Cornerstone3DTools segmentation state does not render it on the viewports. Cornerstone3DTools have decoupled Segmentation from a Segmentation Representation. In short, the Segmentation has the necessary data for rendering different Segmentation Representations such as Labelmap, Contour (not supported yet, see roadmap). So you can have multiple representation of a single Segmentation. Read more at the end of this tutorial.

Let's create a rendering engine and add viewports, and let the ToolGroup know about the viewports it is acting on:

// Instantiate a rendering engine
const renderingEngineId = 'myRenderingEngine';
const renderingEngine = new RenderingEngine(renderingEngineId);

// Create the viewports
const viewportId1 = 'CT_AXIAL';
const viewportId2 = 'CT_SAGITTAL';
const viewportId3 = 'CT_CORONAL';

const viewportInputArray = [
  {
    viewportId: viewportId1,
    type: ViewportType.ORTHOGRAPHIC,
    element: element1,
    defaultOptions: {
      orientation: Enums.OrientationAxis.AXIAL,
    },
  },
  {
    viewportId: viewportId2,
    type: ViewportType.ORTHOGRAPHIC,
    element: element2,
    defaultOptions: {
      orientation: Enums.OrientationAxis.SAGITTAL,
    },
  },
  {
    viewportId: viewportId3,
    type: ViewportType.ORTHOGRAPHIC,
    element: element3,
    defaultOptions: {
      orientation: Enums.OrientationAxis.CORONAL,
    },
  },
];

renderingEngine.setViewports(viewportInputArray);

toolGroup.addViewport(viewportId1, renderingEngineId);
toolGroup.addViewport(viewportId2, renderingEngineId);
toolGroup.addViewport(viewportId3, renderingEngineId);

Let's set the volume to load and set it on the viewports

/ Set the volume to load
  volume.load();

  // Set volumes on the viewports
  await setVolumesForViewports(
    renderingEngine,
    [
      {
        volumeId,
        callback: ({ volumeActor }) => {
          // set the windowLevel after the volumeActor is created
          volumeActor
            .getProperty()
            .getRGBTransferFunction(0)
            .setMappingRange(-180, 220);
        },
      },
    ],
    [viewportId1, viewportId2, viewportId3]
  );

Finally, we create a labelmap representation of the segmentation and add it to the toolGroup

// Add the segmentation representation to the toolGroup
await segmentation.addSegmentationRepresentations(toolGroupId, [
  {
    segmentationId,
    type: csToolsEnums.SegmentationRepresentations.Labelmap,
  },
]);

// Render the image
renderingEngine.renderViewports([viewportId1, viewportId2, viewportId3]);

Final code​

// Get Cornerstone imageIds and fetch metadata into RAM
const imageIds = await createImageIdsAndCacheMetaData({
  StudyInstanceUID:
    '1.3.6.1.4.1.14519.5.2.1.7009.2403.334240657131972136850343327463',
  SeriesInstanceUID:
    '1.3.6.1.4.1.14519.5.2.1.7009.2403.226151125820845824875394858561',
  wadoRsRoot: 'https://d3t6nz73ql33tx.cloudfront.net/dicomweb',
});

const content = document.getElementById('content');

const viewportGrid = document.createElement('div');
viewportGrid.style.display = 'flex';
viewportGrid.style.flexDirection = 'row';

// element for axial view
const element1 = document.createElement('div');
element1.style.width = '500px';
element1.style.height = '500px';

// element for sagittal view
const element2 = document.createElement('div');
element2.style.width = '500px';
element2.style.height = '500px';

// element for coronal view
const element3 = document.createElement('div');
element3.style.width = '500px';
element3.style.height = '500px';

viewportGrid.appendChild(element1);
viewportGrid.appendChild(element2);
viewportGrid.appendChild(element3);

content.appendChild(viewportGrid);

addTool(SegmentationDisplayTool);
addTool(BrushTool);

const volumeName = 'CT_VOLUME_ID';
const toolGroupId = 'CT_TOOLGROUP';
const volumeLoaderScheme = 'cornerstoneStreamingImageVolume';
const volumeId = `${volumeLoaderScheme}:${volumeName}`;
const segmentationId = 'MY_SEGMENTATION_ID';
// Define tool groups to add the segmentation display tool to
const toolGroup = ToolGroupManager.createToolGroup(toolGroupId);

// Segmentation Tools
toolGroup.addTool(SegmentationDisplayTool.toolName);
toolGroup.addTool(BrushTool.toolName);
toolGroup.setToolEnabled(SegmentationDisplayTool.toolName);

toolGroup.setToolActive(BrushTool.toolName, {
  bindings: [{ mouseButton: csToolsEnums.MouseBindings.Primary }],
});

// Define a volume in memory for CT
const volume = await volumeLoader.createAndCacheVolume(volumeId, {
  imageIds,
});

// Create a segmentation of the same resolution as the source data for the CT volume
await volumeLoader.createAndCacheDerivedSegmentationVolume(volumeId, {
  volumeId: segmentationId,
});

// Add the segmentations to state
segmentation.addSegmentations([
  {
    segmentationId,
    representation: {
      // The type of segmentation
      type: csToolsEnums.SegmentationRepresentations.Labelmap,
      // The actual segmentation data, in the case of labelmap this is a
      // reference to the source volume of the segmentation.
      data: {
        volumeId: segmentationId,
      },
    },
  },
]);

// Instantiate a rendering engine
const renderingEngineId = 'myRenderingEngine';
const renderingEngine = new RenderingEngine(renderingEngineId);

// Create the viewports
const viewportId1 = 'CT_AXIAL';
const viewportId2 = 'CT_SAGITTAL';
const viewportId3 = 'CT_CORONAL';

const viewportInputArray = [
  {
    viewportId: viewportId1,
    type: ViewportType.ORTHOGRAPHIC,
    element: element1,
    defaultOptions: {
      orientation: Enums.OrientationAxis.AXIAL,
    },
  },
  {
    viewportId: viewportId2,
    type: ViewportType.ORTHOGRAPHIC,
    element: element2,
    defaultOptions: {
      orientation: Enums.OrientationAxis.SAGITTAL,
    },
  },
  {
    viewportId: viewportId3,
    type: ViewportType.ORTHOGRAPHIC,
    element: element3,
    defaultOptions: {
      orientation: Enums.OrientationAxis.CORONAL,
    },
  },
];

renderingEngine.setViewports(viewportInputArray);

toolGroup.addViewport(viewportId1, renderingEngineId);
toolGroup.addViewport(viewportId2, renderingEngineId);
toolGroup.addViewport(viewportId3, renderingEngineId);

// Set the volume to load
volume.load();

// Set volumes on the viewports
await setVolumesForViewports(
  renderingEngine,
  [
    {
      volumeId,
    },
  ],
  [viewportId1, viewportId2, viewportId3]
);

// // Add the segmentation representation to the toolGroup
await segmentation.addSegmentationRepresentations(toolGroupId, [
  {
    segmentationId,
    type: csToolsEnums.SegmentationRepresentations.Labelmap,
  },
]);

// Render the image
renderingEngine.renderViewports([viewportId1, viewportId2, viewportId3]);

You should be able to draw segmentations with the brush tool

Read more​

Learn more about:

Tip
  • Visit Examples page to see how to run the examples locally.
  • Check how to debug examples in the Debugging section.