GeoS v2.3 User Guide
 

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

 

Opening Screen

Opening Screen

  •  You can open a Medical Volume by clicking on LoadVolume or using Windows File Explorer to drag and drop.

 

Volume Loaded

Volume Loaded

  • 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.

 

 

Segment Labels

 Segment Labels

  • Segmentations are assigned to Segment Labels. These are listed on the left.
  • Use the buttons to Add Segment Label, Load and Save a list of Segment Labels
  • Buttons to the right are for Multi Class Mode and for Uncertainty Map visualization. These are explained further below.
 

Volume Histogram and Window/Level

 

 

  • Histogram shows the volume intensities. It also shows the Window and Level as moving vertical lines.
  • Window and Level can be set using the sliders or the preset values. Computation of Segment depends on Window and Level setting used.
  • Custom settings can also be added to presets. These will be saved automatically

 

 

 

Brush Strokes Added

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

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.

 

 

SegmentInfo Section

SegmentInfo Section

 

SegmentInfo Section 
  • SegmentInfo section provides more information and operations on the selected Segment Label.
  • VoxelValue is a byte marker that would be used to mark the segment mask in a volume when saving. You can edit the VoxelValue.
  • Brush and Segment Volumes can be imported or exported.
  • Report section shows the surface 3d rendering of the segmentation.
  • The measurement of the segmented volume is shown in millilitres.
  • The histogram shows the intensities of the volume extracted by applying the segment mask to the main volume.
  • Notes can be added in the Notes area.
  • The report can be saved as a .json file, which includes all the data points in the report section.
  • The report section can be hidden away to conserve memory.
 
 

 

 

Uncertainty Map

Uncertainty Map 

  • 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 

  • 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 SegmentsImport Multi Class Segments

  • While in MultiClass Mode you can Import a Multi Class Segment Volume. Select the Multi Class Segment Volume to load.

 

 

 
  • You can select which Classes to Import. New Segment Labels will be created for each of the Class imported.
  • You should rename the Segment Labels appropriately.
  • If you have defined a Segment Label Dictionary, Labels can be automatically named according to their Voxel Value by pressing on Auto Rename ButtonAuto Rename Button 
 
  • If a Segment Label Dictionary is defined it would show closest matching label names while you type the name 
 
 

 

 

Completed Multi Class Import, visualized in Multi Class Mode

Completed Multi Class Import, visualized in Multi Class Mode 

 

Importing Brushes to a Segment Label

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.

 

 
  • After selecting the Brush Volume to Load, select a Brush Class to import. This visualizes where the brushes are. You can also scroll through the slices 

 

Importing a Segment volume to a Segment Label

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.

 

  • After selecting the Segment Volume to Load, select a Segment Class to import. This visualizes where the Segment is. You can also scroll through the slices.