Scanfields
A scanfield is the 2D cross section of a ROI at a particular z plane. The discrete set of user defined scanfields defines the volumetric shape of the ROI.
Each scanfield is defined by the following set of properties:
- rectangle: x,y coordinates of the top left corner; width; height
- scan resolution: pixels per line, number of lines
- rotation angle
All coordinates are defined in a normalized full field of view coordinate system, which extends from 0 to 1 in both x and y direction.
Scanfields are defined in a normalized full field of view coordinate system, which is defined by the maximum deflection of the galvanometric mirrors.
ROIs
A ROI is a three dimensional volume defined by a set of one or more scanfields, each at a unique z-level. A ROI which contains only one scanfield stretches from z = -inf..inf. To limit the z extent of the ROI, define at least two second scanfields. Each scanfield is a control point in the shape of the 3D volume. Between control points, scanfields are interpolated. Alternatively, a ROI can exist only at discrete z planes only where scanfields are defined.
x | y | width | height | z | |
---|---|---|---|---|---|
scanfield 1 | 0.1 | 0.1 | 0.2 | 0.2 | 0 |
scanfield 2 | 0.5 | 0.5 | 0.4 | 0.4 | 10 |
A ROI consisting of two user defined scanfields at z=0 and z=10. If needed, scanfields are linearly interpolated for different values of z (red rectangles).
ROI Group
A collection of ROIs forms a ROI Group. During a volume acquisition, ScanImage queries the ROI group to return the scanfields at a particular z plane. ScanImage acquires images for each of the scanfields before moving on to the next z plane.
A ROI Group consisting of two ROIs.
Attachments:
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