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ROI Painter Tools

The ROI Painter tools, shown below, can be used for manual segmentation and for editing regions of interest in 2D and 3D views (see 2D Views and 3D Views).

ROI Painter panel

ROI Painter panel

You should note that the behavior of an ROI Painter tool is determined by its selected settings — Add, Remove, 2D/3D mode, and Use range (see ROI Painter Tool Settings).

ClosedROI Painter Tool Settings

The behavior of an ROI Painter tool is determined by its selected mode and settings.

ROI Painter tool settings
  Description

Add

Hold down Left Ctrl (or your configured Add with key) to add selections to a region of interest. See Configured Actions for the ROI Painter Tools for information about the default keys.

Remove

Hold down Left Shift (or your configured Remove with key) to remove selections from a region of interest. See Configured Actions for the ROI Painter Tools for information about the default keys.

2D mode1

Available for working in 2D views only. In 2D mode, you can add and remove selections on the current slice only.

3D mode2

Available for working in 2D views only. In 3D mode, you can add and remove selections on multiple slices that extend through the volume according to the selected brush size.

Use range

You can use this feature to define a domain of intensity on 2D views, which is highlighted a constant red. Any voxel with a value outside the defined range will not be selectable with any of the ROI Painter tools (see Intensity Ranges and Threshold Segmentations).

Dataset3

Allows you to select the object that you want to work with. For example, if you are working with multi-modality images in a fused view, you can alternate between datasets when you work with the ROI Painter tools. You can also choose to work on the labeled voxels of a region of interest or multi-ROI.

1 Applicable to the Brush, Smart Grid, Path, and Snap tools, as well as the Region tools.
2 Applicable to the Brush and Point & Click tools.
3 Available for the Point & Click and Snap tools in 2D views and for all ROI Painter tools in 3D views.

ClosedWorking with the ROI Painter Tools in 2D Views

This topic describes how to work with the ROI Painter tools in 2D views. See Working with the ROI Painter Tools in 3D Views for information about working in 3D views.

ROI Painter tools for 2D views

 

 Icon Description

Brush

You use the Brush tool to paint selections on 2D views in 2D or 3D mode. You can change the diameter of the brush with the mouse scroll wheel, as well as select a Round or Square brush to work with. See Editing Regions of Interest with the Brush Tools for information about re-assigning labeled voxels from one region to interest to another.

  1. Select the required 2D view.
  2. Select the tool settings — 2D or 3D mode.
  3. Select the Brush tool and a brush type — Round or Square.
  4. Do the following:
    • Hold down Left Ctrl (or your configured Add with key) and then drag to add selections to the current region of interest.
    • Hold down Left Shift (or your configured Remove with key) and then drag to remove selections from the current region of interest.

    You can use the scroll wheel on your mouse to increase or decrease the brush size, if required. The brush size shown onscreen is the radius of the brush.

Smart Grid

You use the Smart Grid tool to fill boundary regions defined by an overlaid grid.

The Smart Grid tool, which provides boundary mask regions that can be filled in a single click to define a region of interest or to edit to a segmentation, takes advantage of a watershed algorithm with distance transform and contrast enhancement to accelerate and optimize segmentation tasks.

NOTE If you are working in fused views, the grid will be computed for the topmost dataset in the Data Properties and Settings panel.

  1. Select the required 2D view.
  2. Select 2D mode.
  3. Select the Smart Grid tool.

    A grid is calculated automatically and then overlaid on the selected 2D view.

  4. Do the following to adjust the grid, if required:
    • Choose a new grid size for the X (horizontal) or Y (vertical) axis in the drop-down menus.
    • Increase or decrease the Sigma value.
    • Click the Reset button if you need to update the grid.
  5. Do the following to add or remove selections:
    • Hold down Left Ctrl (or your configured Add by key) and then click within a region to add all pixels in the region to the current region of interest.
    • Hold down Left Shift (or your configured Remove by key) and then click within a region to remove all pixels in the region from the current region of interest.

    You can use the scroll wheel on your mouse to increase or decrease the brush size.

Path

You use the Path tool to create regions of interest that consist of a single line, one pixel wide. The advantage of using this tool instead of working in Brush mode is the smooth curves that are created.

  1. Select the required 2D view.
  2. Select 2D mode.
  3. Select the Path Brush tool.
  4. Hold down Left Ctrl (or your configured Add with key) and then click and drag on the image to create the path.
  5. Release the configured key to end the path and create the region of interest.

    If required, you can edit the region of interest you created with the Brush tool.

Snap

You use the Snap tool to create a region of interest by simply dragging on a feature of interest in a 2D view. The contour line will automatically snap to the gradient that defines the edges of the region.

  1. Select the required 2D view.
  2. Select 2D mode.
  3. Select the Snap tool.
  4. Select the dataset that will provide the data for calculating the gradient in the drop-down menu.

  5. Do the following:
    • Hold down Left Ctrl (or your configured Add with key) and then drag inside the feature you want to add to the selected region. The contour line will snap to the gradient that defines the edges of the region.

      Release the Seed key to fill the region.

    • Hold down Left Shift (or your configured Remove with key) and then drag inside the feature you want to remove from the selected region. The contour line will snap to the gradient that defines the edges of the region. Release the Seed key to remove pixels from the region.

Point & Click

You use the Point & Click tool to grow regions of interest on 2D views based on the standard deviation of intensity values within the selected dataset and their connectivity. Threshold values are calculated for all pixels within the area of the selected brush in Add mode. In Remove mode, the threshold value is taken from the central point of the brush. You should note that selections may extend through the volume on multiple slices when working with the Point & Click tool.

  1. Select the required 2D view.
  2. Select 3D mode.
  3. Select the Point & Click tool.
  4. Select the dataset that will provide the data for calculating the gradient in the drop-down menu.

    You can also use the Point & Click tool on selected regions of interest and multi-labeled ROIs.

  5. Select a brush size with the mouse scroll wheel.
  6. Do the following:
    • Hold down Left Ctrl (or your configured Add to key) and then click on a representative region of the selected object to add selections to the current region of interest.
    • Hold down Left Shift (or your configured Remove from key) and then click on the current region of interest to remove selections.

Rectangle

You use the Rectangle tool to draw rectangular-shaped regions of interest on 2D views.

  1. Select the required 2D view.
  2. Select 2D mode.
  3. Select the Rectangle tool.
  4. Do the following to add or remove selections:
    • Hold down Left Ctrl (or your configured Add to rectangle key) and then drag in the image to shape and size the rectangular region. Release the configured key to add the selection to the current region of interest.
    • Hold down Left Shift (or your configured Remove from rectangle key) and then drag in the image to remove rectangular selections from the ROI. Release the configured key to remove the selection from the current region of interest.

Ellipse

You use the Ellipse tool to draw circular or oval-shaped regions of interest on 2D views.

  1. Select the required 2D view.
  2. Select 2D mode.
  3. Select the Ellipse tool.
  4. Do the following to add or remove selections:
    • Hold down Left Ctrl (or your configured Add to ellipse key) and then drag in the image to shape and size the elliptical region. Release the configured key to add the selection to the current region of interest.
    • Hold down Left Shift (or your configured Remove from ellipse key) and then drag in the image to remove elliptical selections from the ROI. Release the configured key to remove the selection from the current region of interest.

Polygon

You use the Polygon tool to draw regions of interest shaped as polygons on 2D views.

  1. Select the required 2D view.
  2. Select 2D mode.
  3. Select the Polygon tool.
  4. Do the following to add or remove selections:
    • Hold down Left Ctrl (or your configured Add to polygon key) and then click on a succession of points to define the contour of the region. Release the configured key to add the selection to the current region of interest.
    • Hold down Left Shift (or your configured Remove from polygon key) and then click on a succession of points to define the contour of the region that will be removed from the ROI. Release the configured key remove the selection from the current region of interest.

Freehand

You use the Freehand tool to draw free-form regions of interest on 2D views.

  1. Select the required 2D view.
  2. Select 2D mode.
  3. Select the Freehand tool.
  4. Do the following to add or remove selections:
    • Hold down Left Ctrl (or your configured Add to freehand key) and then drag to define the required contour. Release the configured key to add the selection to the current region of interest.
    • Hold down Left Shift (or your configured Remove from freehand key) and then drag to define the contour of the region that will be removed from the ROI. Release the configured key to remove the selection from the current region of interest.
ClosedHow to Work with the ROI Painter Tools in 2D Views
  1. Scroll through the image stack and adjust the view so that the area you plan to segment is shown clearly onscreen (see Using the Manipulate Tools).
  2. Click the Segment tab on the left side of the workspace to access the ROI Painter and ROI Tools panels.
  3. Do one of the following:
    • Click the New button in the Basic box on the ROI Tools panel, if you need to create a new ROI.

      Refer to the topic How to Create A New Region of Interest for information about creating new ROIs.

    • Select the region of interest you intend to modify in the Data Properties and Settings panel.
  4. Define a range, optional.

    In this context, any voxel with a value outside the range will not be selectable (see Intensity Ranges and Threshold Segmentations).

  5. Select the tool with which you plan to segment the required region and the tool settings (see ROI Painter Tool Settings).
  6. Segment the image, as required.
ClosedEditing Regions of Interest with the Brush Tools

To edit a segmentation, you can automatically re-assign labeled voxels from one region to interest to another with the Brush tools. For example, in cases in which an automated bone segmentation resulted in voxels corresponding to trabecular bone erroneously labeled as cortical bone or vice versa. In the example below, some trabecular regions (highlighted in blue) were assigned to cortical bone (highlighted in yellow).

Automated segmentation result

You can also choose to work in Exclusive mode with the Brush tools. In this mode, only the labeled voxels belonging to the selected regions of interest will be affected when painting. This option is available on the ROI Painter panel as shown below.

ROI Painter panel

ClosedHow to Re-Assign Labeled Voxels from One ROI to Another
  1. Select the 2D view in which you plan to edit the regions of interest.
  2. Select the required regions of interest on the Data Properties and Settings panel.

    The selected ROIs are identified as (A) and (B).

  3. Select a 2D or 3D Brush on the ROI Painter panel.
  4. Select the Exclusive option, if required.

    In this mode, painting will only be applied to the labeled voxels of the selected regions of interest. Unlabeled voxels will not be painted.

  5. Do the following, as required:
    • Add and re-assign labeled voxels to ROI (A) from ROI (B) by holding down Left Ctrl (or your configured Add with key) and then painting.

      As shown below, only voxels highlighted in yellow are re-assigned to those highlighted in blue when painting in Exclusive mode.

    • Remove and re-assign labeled voxels from ROI(A) to ROI(B) by holding down Left Shift (or your configured Remove with key) and then painting.
ClosedWorking with the ROI Painter Tools in 3D Views

This topic describes how to work with the ROI Painter tools in 3D views. See Working with the ROI Painter Tools in 2D Views for information about working in 2D views.

You must select the object — None, Dataset, or Region of Interest — you want to work on when you use the ROI Painter tools in 3D views. These working areas are described in the following table.

Working area for 3D views

 

Description

None

Lets you work on all voxels within the shape of the selected region of interest.

Dataset

Lets you work on all visible voxels of the selected dataset. You can adjust window leveling to help isolate objects that you need to select (see Window Leveling).

Region of interest

Lets you work on all labeled voxels of the selected region of interest or multi-ROI.

Refer to the following for information about working with the ROI Painter tools in 3D views.

ROI Painter tools for 3D views

 

   Description

Brush

You use the Brush tool to paint selections. You can change the diameter of the brush with the mouse scroll wheel, as well as select a Round or Square brush to work with.

  1. Select the required 3D view.
  2. Select the Brush tool and a brush type — Round or Square.
  3. Select a working area in the drop-down menu (see Working area for 3D views).
  4. Do the following:
    • Hold down Left Ctrl (or your configured Add with key) and then drag to add selections to the current region of interest.
    • Hold down Left Shift (or your configured Remove with key) and then drag to remove selections from the current region of interest.

    You can use the scroll wheel on your mouse to increase or decrease the brush size, if required. The brush size shown onscreen is the radius of the brush.

Point & Click

You use the Point & Click tool to grow regions of interest on 3D views based on the standard deviation of intensity values within the selected dataset and their connectivity. Threshold values are calculated for all pixels within the area of the selected brush in Add mode. In Remove mode, the threshold value is taken from the central point of the brush. You should note that selections may extend through the volume on multiple slices when working with the Point & Click tool.

  1. Select the required 3D view.
  2. Select the working area in the drop-down menu that will provide the threshold values (see Working area for 3D views).
  3. Do the following:
    • Hold down Left Ctrl (or your configured Add to key) and then click on a representative region of the selected object to add selections to the current region of interest.
    • Hold down Left Shift (or your configured Remove from key) and then click on the current region of interest to remove selections from the current region of interest.

Rectangle

You use the Rectangle tool to draw rectangular-shaped regions of interest in 3D views.

  1. Select the required 3D view.
  2. Select the Rectangle tool.
  3. Select a working area in the drop-down menu (see Working area for 3D views).
  4. Do the following to add or remove selections:
    • Hold down Left Ctrl (or your configured Add to rectangle key) and then drag in the image to shape and size the rectangular region. Release the configured key to add the selection to the current region of interest.
    • Hold down Left Shift (or your configured Remove from rectangle key) and then drag in the image to remove rectangular selections from the ROI. Release the configured key to remove the selection from the current region of interest.

Ellipse

You use the Ellipse tool to draw circular or oval-shaped regions of interest in 3D views.

  1. Select the required 3D view.
  2. Select the Ellipse tool.
  3. Select a working area in the drop-down menu (see Working area for 3D views).
  4. Do the following to add or remove selections:
    • Hold down Left Ctrl (or your configured Add to ellipse key) and then drag in the image to shape and size the elliptical region. Release the configured key to add the selection to the current region of interest.
    • Hold down Left Shift (or your configured Remove from ellipse key) and then drag in the image to remove elliptical selections from the ROI. Release the configured key to remove the selection from the current region of interest.

Polygon

You use the Polygon tool to draw regions of interest shaped as polygons on 3D views.

  1. Select the required 3D view.
  2. Select the Polygon tool.
  3. Select a working area in the drop-down menu (see Working area for 3D views).
  4. Do the following to add or remove selections:
    • Hold down Left Ctrl (or your configured Add to polygon key) and then click on a succession of points to define the contour of the region. Release the configured key to add the selection to the current region of interest.
    • Hold down Left Shift (or your configured Remove from polygon key) and then click on a succession of points to define the contour of the region that will be removed from the ROI. Release the configured key remove the selection from the current region of interest.

Freehand

You use the Freehand tool to draw free-form regions of interest on 3D views.

  1. Select the required 3D view.
  2. Select the Freehand tool.
  3. Select a working area in the drop-down menu (see Working area for 3D views).
  4. Do the following to add or remove selections:
    • Hold down Left Ctrl (or your configured Add to freehand key) and then drag to define the required contour. Release the configured key to add the selection to the current region of interest.
    • Hold down Left Shift (or your configured Remove from freehand key) and then drag to define the contour of the region that will be removed from the ROI. Release the configured key to remove the selection from the current region of interest.
  1. Select the required 3D view and adjust the rendering so that the area you plan to segment is shown clearly onscreen.
  2. Click the Segment tab on the left side of the workspace to access the ROI Painter and ROI Tools panels.
  3. Do one of the following:
    • Click the New button in the Basic box on the ROI Tools panel, if you need to create a new ROI.

      Refer to the topic How to Create A New Region of Interest for information about creating new ROIs.

    • Select the region of interest you intend to modify in the Data Properties and Settings panel.
  4. Make sure that the region of interest you plan to modify is set to visible in 3D.
  5. Adjust the opacity settings of the highlight, ROI, and dataset in the 3D opacity box on the Data Properties and Settings panel, recommended.

  6. Select the tool with which you plan to segment the image and the tool settings.
  7. Select a working area in the drop-down menu (see Working area for 3D views).
  8. Segment the image, as required.

    Refer to the table ROI Painter tools for 3D views for information about applying the ROI Painter tools in 3D views.

ClosedConfigured Actions for the ROI Painter Tools

A number of configured actions and keyboard shortcuts are available for using the ROI Painter tools. The default settings for each ROI Painter tool are listed below.

ClosedConfigured Actions for the Brush Tool
Default configured actions for Brush tool

Action

Key

Mouse

Add with circular brush

Left Ctrl

Left mouse

Remove with circular brush

Left Shift

Left mouse

Add with rectangular brush

Left Ctrl

Left mouse

Remove with rectangular brush

Left Shift

Left mouse

Increase circular brush size (in ROI Painter)

-

Mouse wheel up

Decrease circular brush size (in ROI Painter)

-

Mouse wheel down

Increase rectangular brush size (in ROI Painter)

-

Mouse wheel up

Decrease rectangular brush size (in ROI Painter)

-

Mouse wheel down

Switch to circular brush add

Left Ctrl

-

Switch to circular brush remove

Left Shift

-

Switch to rectangular brush add

Left Ctrl

-

Switch to rectangular brush remove

Left Shift

-
ClosedConfigured Actions for the Smart Grid Tool
Default configured actions for Smart Grid tool

Action

Key

Mouse

Add by Smart Grid segmentation

Left Ctrl

Left mouse

Remove by Smart Grid segmentation

Left Shift

Left mouse

Increase brush size in Smart Grid segmentation

-

Mouse wheel up

Decrease brush size in Smart Grid segmentation

-

Mouse wheel down

Switch to add by Smart Grid segmentation mode

Left Ctrl

-

Switch to remove by Smart Grid segmentation mode

Left Shift

-
ClosedConfigured Actions for the Path Tool
Default configured actions for Path tool

Action

Key

Mouse

Add with Path brush

Left Ctrl

Left mouse

Switch to Path brush add

Left Ctrl

-
ClosedConfigured Actions for the Snap Tool
Default configured actions for Snap tool

Action

Key

Mouse

Add with Snap brush

Left Ctrl

Left mouse

Remove with Snap brush

Left Shift

Left mouse

Increase circular Snap brush size (in ROI Painter)

-

Mouse wheel up

Decrease circular Snap brush size (in ROI Painter)

-

Mouse wheel down

Switch to Snap brush add

Left Ctrl

-

Switch to Snap brush remove

Left Shift

-
ClosedConfigured Actions for the Point & Click Tool
Default configured actions for Point & Click tool

Action

Key

Mouse

Add to Point & Click

Left Ctrl

Left mouse

Remove from Point & Click

Left Shift

Left mouse

Increase Point & Click brush size (in ROI Painter)

-

Mouse wheel up

Decrease Point & Click brush size (in ROI Painter)

-

Mouse wheel down

Activate Point & Click add

Left Ctrl

-

Activate Point & Click remove

Left Shift

-
ClosedConfigured Actions for the Region Tools
Default configured actions for Region tools

Action

Key

Mouse

Add to ellipse (in ROI Painter)

Left Ctrl

Left mouse

Remove from ellipse (in ROI Painter)

Left Shift

Left mouse

Add to freehand (in ROI Painter)

Left Ctrl

Left mouse

Remove from freehand (in ROI Painter)

Left Shift

Left mouse

Add to polygon (in ROI Painter)

Left Ctrl

Left mouse

Remove from polygon (in ROI Painter)

Left Shift

Left mouse

Add to rectangle (in ROI Painter)

Left Ctrl

Left mouse

Remove from rectangle (in ROI Painter)

Left Shift

Left mouse

Increase circular brush size (in ROI Painter)

 

Mouse wheel up

Decrease circular brush size (in ROI Painter)

 

Mouse wheel down

Increase point and click brush size (in ROI Painter)

 

Mouse wheel up

Decrease point and click brush size (in ROI Painter)

 

Mouse wheel down

Increase point and click brush size (in ROI Painter)

 

Mouse wheel up

Decrease point and click brush size (in ROI Painter)

 

Mouse wheel down

Increase rectangular brush size (in ROI Painter)

 

Mouse wheel up

Decrease rectangular brush size (in ROI Painter)

 

Mouse wheel down

Switch to add to ellipse mode (in ROI Painter)

Left Ctrl

 

Switch to remove from ellipse mode (in ROI Painter)

Left Shift

 

Switch to add to freehand mode (in ROI Painter)

Left Ctrl

 

Switch to remove from freehand mode (in ROI Painter)

Left Shift

 

Switch to add to polygon mode (in ROI Painter)

Left Ctrl

 

Switch to remove from polygon mode (in ROI Painter)

Left Shift

 

Switch to add to rectangle mode (in ROI Painter)

Left Ctrl

 

Switch to remove from rectangle mode (in ROI Painter)

Left Shift

 
See Configurable Actions for information about modifying the default actions for the ROI Painter tools.

 

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Dragonfly Version 4.1

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