Segmentation Tools

Overview of all the segmentation tools


The brush tool has two modes - 2D and 3D (toggled on the right-side panel). The 2D brush is a circle, and the 3D brush is a sphere that segments across slices. You can adjust the size of the brush using the slider on the right-side panel, or the w & s hotkeys.
Left click + drag to segment and right click + drag to erase.


The Pen tool has two modes - 2D and 3D (toggled on the right-side panel). The pen tool allows you to annotate using a free-form contour. In 3D mode, the free-form contour is extruded above and below the current slice.
Left click + drag to add a segment region and Left click + drag to remove a region.

Region Growing

Region growing is a semi-automated segmentation tool that uses image intensity information to segment regions. By clicking and holding in a region, the segmentation will grow outward from the seed point (where you clicked). The longer you hold, the longer the region will grow.
Right click + hold to segment, left click + hold to erase.

Contour Tool

The contour tool allows you to draw outlines of your regions quickly and then interpolate between slices.
To activate it - (a) select the tool from the top bar, (b) press the "k" hotkey, or (c) search for the Contour tool in the command bar.

Creating a contour & interpolating

  1. 1.
    To get started, click on a 2D viewport. You can click and drag or add points one click at a time.
  2. 2.
    To close/complete the contour, click the end node.
  3. 3.
    You can then change the slice and repeat the process. If you skip slices, the in-between slices will be interpolated.

Editing a contour

To edit, hover near the edge of your region and click and drag to draw a new segment. Editing an interpolated contour will automatically adjust the neighboring interpolated contours.

Rasterize to complete the contour

When you finish your contour, you must convert it to a pixel mask. This process is called "rasterization." There is a button on the right panel to do this, or you can use the Shift+Enter hotkey.

Smart contouring

Our smart contour tool automatically draws a contour around a region of interest. To use it, while the contour tool is selected, press alt/option and hover near the boundary of an object. Click to confirm the automatic contour.
For bumpy boundaries, you can attempt to smooth out the contour by holding and dragging, adjust the distance you drag to make the contour less or more smooth.
In the video above, the hotkey is referenced as "Command or Control" but the correct key is "Alt or Option"

Island Removal

Island removal removes islands of segmentations. Click on any "island" segmentation to remove it. On the right side context panel, you can activate "keep currently selected" to remove all islands except the one you clicked on.

Hole Filling

Holde filling iteratively fills small holes in your segmentation. Click anywhere on the canvas to start filling the small holes.
Hole filling is designed to fill small holes. For larger holes, you may need to run it more than once to close the hole completely.
For large volumes, 3D hole filling can be very computationally expensive. If your data has more than 800 slices, we recommend only using 2D hole filling.

Paint Bucket

Paint bucket is helpful for closing single large holes. With the paint bucket tool selected, click in any large hole to fill it automatically.


Thresholding allows you to bound the intensity values in your image that will get segmented. Thresholding can be combined with any of the tools above to allow for faster segmentation.
To activate thresholding, select the threshold filter from the top bar and select the threshold region from the right sidebar slider. You can also interactively select the threshold region by toggling "Threshold Range Selector", then left-click on the canvas to add a region and right-click on the canvas to remove it.
As long as the threshold filter is active, i.e. highlighted on the top bar and present on the right panel, the volume will remain thresholded.
You can disable the flashing preview if it is distracting from the right sidebar.