Missing feature: magnification

[bmorris3]

The current implementation of shampoo doesn't account for the magnification of the main objective, so the propagation distances aren't correct.

The propagation distance should be divided by the square of the MO's magnification, which I've been told is usually 19-20 for shampoo.

[bmorris3]

@jkentwallace – So far, shampoo's propagation distance doesn't account for the magnification of the main objective. Jay once told me that to account for the magnification properly, all I should do is divide the propagation distances by the square of the magnification of the MO. Is that correct? What is the magnification of the MO that we've typically been using?

Once this is corrected, we can put physical scales on the reconstructed images.

[jkentwallace]

Brett, Currently the reconstruction is happening in 'CCD' space. The transverse distance is given by the pixel physical size x the number of pixels. The propagation distance is longitudinal distance in the same CCD space. When going to 'sample' space -> which is the space where the specimen is in the chamber, then two steps need to be taken: the transverse distance is downscaled by the magnification. So pixel size at specimen = pixel size/magnification. However, longitudinal distances get reduced by magnification squared. So, for instance, 1 cm of propagation distance = 1 cm/mag^2 at the specimen. Finally, the 'resolution' of the longitudinal step size is called the depth of focus. The depth of focus = 2 wavelength * f/# ^2 = 2 wavelength * (1/2 NA)^2 = (wavelength/2) NA^2. This is in 'specimen' space. For the common mode system, the nominal magnification is 19.7.