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This documentation is for a legacy ScanImage version. The current documentation is ScanImage 2019.
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For an overview of the ScanImage Roi concept, please review the article Scanfields, ROIs, ROI Groups.

ScanImage organizes Rois and Scanfields in a hierarchy. The root of this hiearchy is a RoiGroup object. Each RoiGroup object can contain multiple Rois, and each Roi can contain multiple scanfields.

Create a RoiGroup and add Rois
Manipulate RoiGroup

 

Each Roi, RoiGroup and Scanfield object has a unique identifier 'uuid', which is a human readable string. For performance reasons, a 64-bit integer value 'uuiduint64' is derived from 'uuid', which can be used to identify the object in the roigroup.

Manipulate RoiGroup using uuiduint64
Clear RoiGroup
RoiGroup hierarchy
  • RoiGroup
    • Roi
      • Scanfield, z = 0
      • Scanfield, z = 0.2
      • Scanfield, z = 0.3
    • Roi
      • Scanfield, z = 0.1
      • Scanfield, z = 0.5
    • Roi
      • Scanfield, z = 0.4
      • Scanfield, z = 1
Manipulate Rois

 

Scanfields

Each Roi can contain one or more Scanfields. A Scanfield is a 2D cross-section of the 3D Roi at a particular z level. ScanImage currently has multiple types of scanfields.

  • RotatedRectangle - defines an imaging area
  • StimulusField - defines a stimulus path
  • IntegrationField - defines a region, where image data is integrated for online analysis

All fields are defined in the ScanImage Coordinate Systems coordinate system.

 

Rotated Rectangle Imaging Scanfield

 

Rotated Rectangle Imaging Scanfield

 

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