Automatically changing image calibration/scaling when you have additional magnification changing optics

Usage & Issues
#1

Hi all,

We use a few stereo microscopes to capture images and I was wondering if there is a way to calculate the image um/pixel values without having to just have a massive list of the all the possible lens, zoom, c-mount combinations in one group called “lens/objective”. For us if we use 3 lenses and a zoom range with 12 positions then we need 36 entries in the lens group. If you could have one group for lens, one for zoom and one for any additional magnification e.g. C-mount you could make the calibration be a calculation based on the values currently set in the 3 groups but would require somewhere where this calculation influences the stored pixel size calibration values that these groups would refer to. Rather than you feeding micro-manager the end result of the pixel size calculation which we had to do for each lens/zoom combination why not have micro-manager do the arithmetic based on values in the groups that needed to be take account of e.g. groups named lens, zoom, additional mag of course somewhere you’d also need to store the binning value and camera pixel size to calculate this.

Thanks for the help,

Matt

#2

I think i’ve answered my own question sort of. I can see with the demo hub i can have lens and zoom devices and then i can use the variable optovar for the C-mount mag then i just need to make the pixel size calibrations based on the former two parameters and the optovar automatically adjusts the calculation. You still need to feed all the lens/zoom um/pixel values into the pixel size calibration table though.

#3

You can make a second Optovar and name it “Zoom”. That way the only pixel size calibrations needed are for your three objectives. Set the values for the Optovar and Zoom correctly (if they are not encoded using the demo devices), and MM should know the correct pixel size. Binning is always automatically included in that calculation.