Use Case Customizable Magic Wand

Create, edit, and build up segmentation objects with a customizable Magic Wand

Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms, Raw data kindly provided by Srigokul Upadyayula, Tsung-Li Liu, Tom Kirchhausen, and Eric Betzig.
 

Manual segmentation tasks are greatly assisted by a flexible Magic Wand tool that works on user defined regions of interest in 2D or 3D.
This new workflow allows users to leverage several segmentation modes, precisely define boundaries for the Magic Wand, and easily overwrite an unsatisfactory result (by pressing the alt key while picking pixels).
The Magic Wand works on bright objects, dark objects, and objects highlighted within a Range.
You can select any number of channels on which the Magic Wand will compute. This is quite helpful if each channel is only highlights pieces of the desired whole object.
Objects made by the Magic Wand receive a special tag in the objects database and, like other objects, are editable. By applying the Merge function to Magic Wand objects it’s possible to build up intricate 3D structures in complex images.


Step1

Setup the Magic Wand

Click on the Magic Wand icon to enable the tool then configure it for your image. Once the configuration is set, draw a box around the region you will work on. The box automatically extends in 3D.

Step2

Click on the image to create objects

Use the Magic Wand directly on the image to make 2D or 3D objects.  If 3D mode is enabled, the objects with extend in X, Y, and Z.  If you don’t like an object, ALT + left-click will create a new object that overwrites the previous one in the database.

 

Step3

Merge objects

Hard-to-solve segmentation problems are resolved by carefully parameterizing the Magic Wand and selecting regions of interest.Adjacent 3D objects are easily merged into one with Merge objects tool.

 


Other Magic Wand Scenarios

Tolerance Range Mode (Example: X-Ray imagery)
Setting a Tolerance Range enables the Magic Wand to segment objects within an intensity range. This is a powerful way to separate different kinds of objects in the image. Again, Merging is used to build the larger structure from its component parts.

Bright Objects Mode (Example: positive whole-object fluorescence)
This mode will grab objects above the intensity value touched by the Magic Wand. In combination with Merging, it’s possible to quickly segment long and/or windy features of interest.

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