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Segment blob in 3D Viewer

1,066 bytes added, 13:05, 15 February 2011
Docs for segment blob in 3D Viewer
Running the plugin "Plugins - Segmentation - Segment blob in 3D Viewer" will add capabilities to all existing 3D Viewer windows. A new 3D Viewer window opens if none are already open.

[[Image:Blob-segmentation.jpg|thumb|left|232px|Segment blob in 3D Viewer: example of resulting mesh (in green) overlaid on the original image volume (the sample file "bat cochlea volume").]]

= Segmenting a blob =

Step 1: add an image volume from "File - Add content".

Step 2: select the '''magic wand''' tool.

Step 3: click on a bright place of an image volume.

A results window will open with surface and volume measurements, and the 3d coordinates of the blob.

= Canceling an ongoing segmentation =

Push the ESC key. You may have to do so while having the Fiji toolbar window activated.

= Adjusting parameters of the segmentation =

Internally, the [[Level Sets]] plugin is used. To adjust its many parameters, do a shift+click with the magic wand. The dialog will open; it's the same dialog as shown in the [[Level Sets]] documentation page.

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