Created by Lawrence Niu on May 07, 2019

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

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.

Icon

The scanfields that you add to a ROI do not specify the z planes that will actually be imaged when you start an acquisition. The scanfields are only defining the shape of the 3D volume. The z planes to be imaged are set up through the FastZ GUI. For each z plane to be imaged, ScanImage will look at the current ROI group to determine what ROIs exist at that z plane and extract the scanfield to be imaged.

Ex: In the example ROI on the left, scanfields are are defined at z planes of 0 and 10. For this example, suppose the user sets up a fast Z for 4 slices, 4 steps (microns) per slice. The actual z planes that will be imaged would be 0, 4, 8, and 12. The user defined scanfield 1 would be imaged at z plane 0, while interpolated scanfields between 0 and 10 would be imaged at z of 4 and 8. Nothing would be imaged at z of 12 because the ROI only exists between the top and bottom scanfields.

ROIs

 

 xywidthheight

z

scanfield 10.10.10.20.20
scanfield 20.50.50.40.410

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.

ROI Group

 

A ROI Group consisting of two ROIs.

Attachments:

RoiGroup.png (image/png)
mROI Volume.png (image/png)
mROI Full FOV.png (image/png)
FOV vs ROIs.png (image/png)
FOV vs ROIs.svg (image/svg+xml)
mROI Interpolation.png (image/png)