Camera to Stage Mapping problems on upright microscope

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1

Hi,
I’m currently using v3 version of server and have both upright and low cost versions of Openflexure microscope.
In upright version after calibrating both camera and stage “click to move” function works as intended but, when using slide scan function i noticed stage make very small moves and resultant stitched images are overlapped images of very close areas.
Here is example of stitched image:

scan_0001_stitched
scan_0001_stitched872×684 304 KB

Calibration details of current microscope:

  • Current CSM Matrix: [ [ -4.387, 0.044 ], [ -0.108, -4.161 ] ]
  • Pixels per motor step: 0.076
  • Full field of view: [ 62, 47 ] motor steps

Here is calibration details of other low cost microscope:

  • Current CSM Matrix: [ [ 0.011, 4.562 ], [ -4.971, 0.047 ] ]
  • Pixels per motor step: 4.767
  • Full field of view: [ 3909, 2936 ] motor steps

I also have a high resulotion with upright configuration that has similar problem which is why i think it is related to upright configuration.

Thanks in advance.
Edit: Edited lost microscope to low cost microscope.

2

In your CSM Matrix the x and y axes are swapped in the two microscopes. This should be able to be corrected in software, but there could be a problem with it. Could you check that the microscopes have x and y motors plugged in the correct channels? There was also an issue in very early Sangaboard firmware that switched x and z axes, but I am pretty sure that the server v3-alpha1 throws an error if you have old firmware.

Edit: Thinking about the geometry, the upright rotates the optics 180 degrees about the front-back axis of the microscope. This swaps x and y axes in the mecanical system, as your CSM shows. So you would need to try putting the x motor into the y socket on the Sangaboard and vice vesra to see if that is the problem

3

After swapping between x and y motors, problem is solved.
Current calibration details are:

  • Current CSM Matrix: [ [ 0.037, -3.936 ], [ -4.267, -0.095 ] ]
  • Pixels per motor step: 4.101
  • Full field of view: [ 3363, 2526 ] motor steps

Thanks @WilliamW.