Segmentation and Other Tools

Segmentation Tools

Brush Tool

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.
Brush Tool Overview

Pen Tool

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 Right click + drag to remove a region.
Pen Tool Overview

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.
Grow Tool Overview

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 Contour 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 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 with a process called "rasterization". To rasterize your contour, you can use the Shift+Enter hotkey or the Rasterize button in the right hand Context Panel.

Smart Contouring

Our Smart Contour Tool automatically draws a contour around a region of interest. To use Smart Contouring, make sure the Contour Tool is selected, press ctrl+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.
Contour Tool Overview

Hole Filling

The Hole Filling Tool iteratively fills small holes in your segmentation. Click anywhere on the canvas to start filling in small holes.
Hole filling is designed to fill small holes. For larger holes, you may need to run the Hole Filling Tool more than once.
Hole Filling Overview
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

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

Island Removal

Island Removal deletes islands of segmentations. Simply click on any "island" segmentation to remove it. Conversely, you can enable Keep Currently Selected in the right hand Context Panel to remove all of the islands except the one you clicked on.
Island Tool Overview

Merge Tool

The Merge Tool allows you to transform one type of segmentation island into another through a "merging" process. With Segmentation X selected, enable the Merge Tool and click on an island of Segmentation Y to merge the island to Segmentation X.

Fast Automated Segmentation Tool (F.A.S.T. ⚡️)

The Fast Automated Segmentation Tool (F.A.S.T.) is an automatic segmentation tool powered by Meta AI's Segment Anything Model that allows users to rapidly generate 2D and 3D segmentations.
F.A.S.T. Overview
F.A.S.T. is powerful because of the way users can prompt the tool to generate an accurate segmentation in real time. Under the hood, there are two components to the system:
  1. 1.
    Image encoding, which takes place on the server side. The result of image encoding is embeddings, which are special vector representations of the images that are useful for machine learning.
  2. 2.
    Segmentation decoding, which takes place in the browser in real time.
To enable F.A.S.T. for your team, please do the following:
  1. 1.
    Request access at
  2. 2.
    Within a Project, navigate to the Tool Settings page and enable F.A.S.T.

Generating 2D Segmentations with F.A.S.T.

To start segmenting, create a segmentation instance, select the F.A.S.T. tool from the top bar or using cmd/ctrl + b. Once the tool is selected, hover over a viewport to start embedding computation for a single slice (you will see a loader spinner on the top right of the viewport). You can prompt F.A.S.T. in a few different ways after the embedding computation is complete:
  1. 1.
    Bounding Box prompts. Click + move mouse + click to draw a bounding box. You will see the segmentation prediction compute in real time while you draw the bounding box.
    1. 1.
      Key point refinement. After you draw the bounding box, you can optionally refine the segmentation by prompting the system with key points. Left click to add regions you want to add to the segmentation. Right click to remove regions from the segmentation prediction.
    2. 2.
      Once you are happy with the segmentation preview, confirm it by using the button on the right panel or shift + enter.
  2. 2.
    Instant click. alt/option + hover over objects to view a prediction preview. If you are satisfied with any preview, click while pressing alt/option to confirm the segmentation.

Generating 3D Segmentations with F.A.S.T.

3D F.A.S.T. allows users to draw Bounding Boxes to define an interpolation range for a 3D structure that is to be annotated.
The process for creating annotations with 3D F.A.S.T. is extremely similar to that of 2D F.A.S.T. You can find a full step-by-step breakdown of how to use 3D F.A.S.T. below.
1. Create a new Instance of your desired Object Label by clicking on the “+” in the left hand toolbar;
2. Select F.A.S.T. in the top of the screen and wait for the embedding computation to complete on Slice X;
3. Create a Bounding Box around the structure you wish to annotate;
4. (Optional) Provide F.A.S.T. with additional input by using LMB/RMB;
5. Navigate to the end of the range that you want to interpolate across (i.e., Slice Y);
6. Repeat Step 3 (and optionally, Step 4) for the structure you wish to annotate on Slice Y;
7. Once you are satisfied with the annotations, press Enter or click on “Finalize” in the right hand toolbar to generate the pixel masks on every slice between Slice X and Slice Y.
Processing times may increase when interpolating across large ranges. However, please note that all subsequent work across the same range should be much faster, as the embedding computations only have to be computed once per slice.
Firewalls, ad blockers, privacy extensions, and any other browser extensions that block HTTP traffic are known to interfere with FAST.

Other Tools


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.
For a more detailed overview of how to incorporate thresholding into your annotation work, please see the relevant documentation.

Linear Pixel Interpolation

In order to toggle linear pixel interpolation while annotating, click on the Command Bar (or use CMD/CTRL+K) and select "Toggle linear pixel interpolation".
Toggling linear pixel interpolation with an MRI scan of the spine

Tool Configuration

Your labeler toolkit can be customized at the Project level by navigating to the Tool Settings page within your Project Settings.
Simply utilize the checkboxes for each tool to:
  • set a custom default tool;
  • restrict/enable 2D and/or 3D annotation;
  • set a default mode (i.e. 2D or 3D);
  • enable/disable a Tool entirely;