This script is associated with a specific msem experiment. The msem experiment comprises 16 "shift". For each "shift", a set of 7 mFOVs is acquired:
..O..O
O..O..O
..O..O
A mFOV is made of 61 sFOVs.
There is a translation offset in the x axis between shift number 1 and shift number 2.
There is the same translation offset between shift n and shift (n+1)
The translation offset is 1/16 of the width of an sFOV, which is about 1 micrometer.
The translation offset between shift 0 and shift 8 is 8/16 = 1/2 of the width of a sFOV
As a first approximation, it could be assumed that the right half of a sFOV does not have any distortion. This second half could be taken as a ground truth to compute the scan correction.
To find the scan distortion, a vertical 10 pixel wide band from the translated image is fit to the non-translated image.
The script
- calculates exponential fits for all beams
- writes the fit results to a .txt file
- creates a montage like below to see the scan distortion on individual beams
The fit results of mFOV 0 are in the repo:
- 8nm_400ns.txt
- 8nm_1600ns.txt
- 4nm_400ns.txt
- 4nm_1600ns.txt
The mean and std of the 3 fit parameters across all 61 beams are shown here for mFOV 0.
