Difference between revisions of "Segmentation Editor"

(duplicated text from neurofly website, images still missing)
(add images from docs on the neurofly website)
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Open the stack containing the structures you want to reconstruct or segment. Go the to the plugins menu and click on "Segmentation Editor". Your stack will be embedded into a segmentation window, and another window opens, which will contain your labels later.
 
Open the stack containing the structures you want to reconstruct or segment. Go the to the plugins menu and click on "Segmentation Editor". Your stack will be embedded into a segmentation window, and another window opens, which will contain your labels later.
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[[File:Segmentation_Editor_1.png]]
  
 
== Material ==
 
== Material ==
  
 
On the left side of the segmentation window, you see a list of available materials. You can extend and modify these materials by right-clicking into the list. For a first start, right-click on Interior, select "Rename" from the popup menu and specify the name of the label you want.
 
On the left side of the segmentation window, you see a list of available materials. You can extend and modify these materials by right-clicking into the list. For a first start, right-click on Interior, select "Rename" from the popup menu and specify the name of the label you want.
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[[File:Segmentation_Editor_2.png]]
  
 
== Labelling ==
 
== Labelling ==
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After selecting the regions to label in each slice, click the I-Button (which is next to the Plus and Minus button). This interpolates if you didn't make selections on each slice. Now activate the "3d" checkbox. It means that the selections of all slices will be asigned to a material, not only the selection of the current slice.
 
After selecting the regions to label in each slice, click the I-Button (which is next to the Plus and Minus button). This interpolates if you didn't make selections on each slice. Now activate the "3d" checkbox. It means that the selections of all slices will be asigned to a material, not only the selection of the current slice.
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[[File:Segmentation_Editor_3.png]]
  
 
Now go to the material list, select the material which you want to asign, and click on the Plus button. That's it.
 
Now go to the material list, select the material which you want to asign, and click on the Plus button. That's it.
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[[File:Segmentation_Editor_4.png]]
  
 
After finishing, click Ok to close the segmentation window. The labels will remain open. You must store them yourself.
 
After finishing, click Ok to close the segmentation window. The labels will remain open. You must store them yourself.
  
 
Have also a look at our 3D viewer if you want to see your result in 3D.
 
Have also a look at our 3D viewer if you want to see your result in 3D.
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[[File:Segmentation_Editor_medulla_r_labels_rotating.gif]]
  
 
== Starting from a macro ==
 
== Starting from a macro ==

Revision as of 04:59, 8 August 2014

Segmentation Editor (ImageJ)
Author Johannes Schindelin, Francois Kusztos, Benjamin Schmid
Maintainer Benjamin Schmid
File VIB_.jar
Source Template:GitLink
Development status stable


Demo video

http://132.187.25.13/home/SegmentationEditor.avi#!objparams#src=imagej%2FSegmentationEditor.avi

(can this be moved here into the wiki as well?)

Start

Open the stack containing the structures you want to reconstruct or segment. Go the to the plugins menu and click on "Segmentation Editor". Your stack will be embedded into a segmentation window, and another window opens, which will contain your labels later.

Segmentation Editor 1.png

Material

On the left side of the segmentation window, you see a list of available materials. You can extend and modify these materials by right-clicking into the list. For a first start, right-click on Interior, select "Rename" from the popup menu and specify the name of the label you want.

Segmentation Editor 2.png

Labelling

Now go through the slices and use ImageJ's selection tools to select the regions you want to label. You don't need to label each slice. When consecutive slices differ only slightly, you can use the built-in interpolation function to label them.

After selecting the regions to label in each slice, click the I-Button (which is next to the Plus and Minus button). This interpolates if you didn't make selections on each slice. Now activate the "3d" checkbox. It means that the selections of all slices will be asigned to a material, not only the selection of the current slice.

Segmentation Editor 3.png

Now go to the material list, select the material which you want to asign, and click on the Plus button. That's it.

Segmentation Editor 4.png

After finishing, click Ok to close the segmentation window. The labels will remain open. You must store them yourself.

Have also a look at our 3D viewer if you want to see your result in 3D.

Segmentation Editor medulla r labels rotating.gif

Starting from a macro

The segmentation editor can now be started from a macro, with a user-defined set of materials. Such a macro would look like this:

// create a new Segmentation Editor
call("Segmentation_Editor.newSegmentationEditor");

// Reset the material list
call("Segmentation_Editor.newMaterials");

// Add a desired materials
call("Segmentation_Editor.addMaterial", "MyMaterial1", 255, 255, 0);
call("Segmentation_Editor.addMaterial", "MyMaterial2", 255, 0, 0);