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Segmentation Workspace

 

  Overview

The Segmentation configuration as it is in medInria v2.0.1 is just a preview of the canvas on which segmentation algorithms will be added in the future. The only algorithm available as the moment of writing is a manual painting tool.

Configuration Layout

The configuration itself has a visalisation area in which any type of layout can be used: Single, Multi, Custom. The segmentation can be run on any View. On top of the toolbox container is a slection toolbox, which contains all the segmentation plugins loaded when medInria was started. At the moment only one called Paint Segmentation is available as a preview. Once an algorithm is chosen, its controsl are visible in a specific toolbox.

All the usual view properties are accessible.

 segmentation-screenshot

Principles

The painting tool will allow 2 colors to be used.

  1. The green colour will be used to fill the inside of the region of interest.
  2. The red colourwill be used to fill the outside of regions

However you don't necesseraly need the second colour. It has been added there first as a seed for an other algorithm needing seed points inside and outside a region. Here you may only use 1 color if you wish.

 

The generated mask will have three values: 0 for non painted values, 1 for green and 2 for red. If you only use green then the value is only one.

 Once you are done, you may export the mask to the database.

PaintSegmentation-screenshot

 

Painting ToolBox

The Paint Toolbox has several buttons and fields.

  1. Select Data: click on that button to select a view. Once you clicked there, click on a view. It will become the view you will paint in.
  2. Reset Data: Allows you to change the active view. Click on an other view after to select the new one.
  3. Clear Mask: Resets the whole mask in the current view.
  4. Inside: Starts to paint with the inside colour. pressing the left button and dragging the mouse will paint the inside colour.
  5. Outside: Starts to paint with the inside colour. pressing the left button and dragging the mouse will paint the inside colour.
  6. Erase: brings up an eraser. Use it to correct painting imprecisions.
  7. Boundery: Uses a mix inside/outside brush.
  8. Brush Radius: Sets the brush's radius using a slider or a spin box.
  9. Save the mask in the temporary database.

SegmentationTB-screenshot

 

Exporting the Mask

Once you have created your database item by clicking on the corresponding button, a mask is usable in the application. However if you want to save it for later use, you are encouraged to save it in the database, or export it to some external storage device.

To do so go to the browser and use the commands there to save or export the data. Be careful to choose a format that allows "unsigned char" values if you try to export it.

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