GeoS is a Windows application for interactive semi automated segmentation of medical images
Created by the Microsoft Research Cambridge InnerEye Medical Image Analysis Project.
Released as part of the Microsoft Research Medical Imaging Initiative.
For more information, downloadable datasets and other tools please visit Medical Imaging at Microsoft Research
For research use only. Not for use in diagnostic or clinical procedures
- You can open a Medical Volume by clicking on LoadVolume or using Windows File Explorer to drag and drop.
- Volume dimensions and Voxel Spacing are displayed on the top.
- Settings for the segmentation computation is on the left under Settings.
- All three views are interactive. Swap any secondary view with the main workspace by clicking on the arrow on the top left.
Volume Histogram and Window/Level
Brush Strokes Added
- Use the keyboard and mouse to add Foreground and Background Brushes.
- You can find the key bindings for all the operations by pressing F1 at anytime.
More Brush Strokes and Segment computed
- Brush strokes can be added in all three views.
- Press F5 to compute the Segment. Press F6 to automatically navigate to the slices that need more brush strokes.
- You can also manually scroll through slices to inspect the Segmentation. Refine the segmentation by adding more brush strokes.
- Click on Manual button on the top menu to draw on the Segment directly. Note that these changes will be erased if you compute segment using brush strokes later.
- Manual segmentation option is not recommended. Instead use Window Level Settings to visualize the area you want to segment, and add more brush strokes.
- Uncertainty map shows the uncertainty of the segment computation.
- It can be visualized by pressing the appropriate button under Segment Labels or by pressing Shift + S.
- Each voxel's computed uncertainty (whether that pixel belong to the segment or not) ranges from 0.0 to 1.0. This is visualized with a gradient of colours.
- Use this map to decide where to put more brush strokes.
Multi Class Segments
- Multi Class Segments are when more than one distinct structures are available in the same Segment Volume or visualization
- Multi Class Mode enables you to visualize all the Segments in the Segment Labels list. This is for visualization only, no drawing or editing is supported in this mode
Import Multi Class Segments
- While in MultiClass Mode you can Import a Multi Class Segment Volume. Select the Multi Class Segment Volume to load.
Completed Multi Class Import, visualized in Multi Class Mode
Importing Brushes to a Segment Label
- A Brush volume can be imported to a Segment Label. This enables sharing of Brush Volumes as well as starting from unfinished work you have previously done.
- Brush volume has to be of the same dimensions as the main Volume.
Importing a Segment volume to a Segment Label
- A Segment Volume can be imported to a Segment Label. Segment Volume has to be of the same dimensions as the main Volume.