Segmentation and Other 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
Left click + dragto segment and
right click + dragto erase.
Brush Tool Overview
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 + dragto add a segment region and
Right click + dragto remove a region.
Pen Tool Overview
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 + holdto segment,
left click + holdto erase.
Grow Tool Overview
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.
- 1.To get started, click on a viewport. You can click and drag or add points one click at a time.
- 2.To close/complete the contour, click the end node.
- 3.You can then change the slice and repeat the process. If you skip slices, the in-between slices will be interpolated.
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.
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+Enterhotkey or the Rasterize button in the right hand Context Panel.
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
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.
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 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
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.
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. 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.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.Segmentation decoding, which takes place in the browser in real time.
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.Bounding Box prompts.
Click + move mouse + clickto draw a bounding box. You will see the segmentation prediction compute in real time while you draw the bounding box.
- 1.Key point refinement. After you draw the bounding box, you can optionally refine the segmentation by prompting the system with key points.
Left clickto add regions you want to add to the segmentation.
Right clickto remove regions from the segmentation prediction.
- 2.Once you are happy with the segmentation preview, confirm it by using the button on the right panel or
shift + enter.
- 2.Instant click.
alt/option + hoverover objects to view a prediction preview. If you are satisfied with any preview, click while pressing
alt/optionto confirm the segmentation.
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.
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
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.
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.
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
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;