Hi everyone,
I use ScanImage 2020 (premium), I am currently working with a galvo-galvo scanner configuration to perform frame scan for calcium functional imaging. My setup involves scanning mROIs groups of rectangular, scattered and rotated ROIs (rotatedRectangles
), which include short dendritic segments.
In the mROI editor, I enter all the properties of the rotated rectangles, such as width, height, rotation, pixels, and pixel ratio. Additionally, in the advanced timing settings of the configuration window, I set all the time parameters, including dwell time, bin factor, sampling rate, and fill fraction. Based on these parameters, the line period is calculated in microseconds (µs) and displayed in the configuration window. Depending on the number of ROI lines within the rectangle, the frame rate in Hz is also calculated and displayed.
Objective:
My goal is to be able to accurately infer the line period (the time it takes to scan a single line of an ROI) from rectangles properties. I have noticed that the relationship is only partially linear, and I need assistance understanding the correct calculation method.
Known Properties:
- Sampling rate: 1.250 MHz (period: 0.0008 ms)
- Pixel bin factor: 4
- Pixel dwell time: 3200 ns
- Rectangular ROIs can be rotated in 2D space
- Fly-to time between ROIs: 1 ms
- Fly-back time at the end of the ROI: 1 ms
Given an example ROI with dimensions (82, 132) the theoretical line period should be:
82 * 3200 ns = 262400 ns # -> 0,2624 ms
However, the actual line period always has an excess time, I am guessing due to the turnaround time needed for the scanner mirrors to slow down and reverse direction at the end of a line.
Software Documentation:
According to ScanImage documentation, this excess time (and space) is referred to as the fill fraction:
ft = 2 * line active acquisition time / scanner period
fs = angle of active acquisition / (2 * scanner angular amplitude)
fs = cos((1 - ft) * π/2)
For my galvo-galvo configuration
ft = 0.9
fs = 0.9
Questions:
- How is line period calculated?
- How is the fill fraction incorporated into the calculation of the line period?
- How should the turnaround time be computed considering the fill fraction and the scanner’s angular velocity?
- Does line period depend on the overall scattered distribution of ROIs?
Thank you in advancefor any help!
Dario