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Remote Focusing Optimization

Open AdvancedImagingUTSW opened this issue 3 years ago • 1 comments

I would like to implement a 2D search to find the best remote focusing offset and amplitude. If we are somewhat close to the best value, it shouldn't be that bad, but we may need to be smarter than that if we are far from the optimum. One additional challenge is that it can be dependent on the focus as a 3rd parameter...

If we were to replicate how I do it manually, it would consist of the following steps:

  1. Set the amplitude of the remote focusing to 0. Offset to 2.5. Could set the laser automatically to a low laser power to reduce bleaching. Could also be smart to see if our counts get too high that our values are non-quantitative (>65,000).
  2. Adjust the focus until we find the narrowest strip of in-focus information. Could run the DCT on a row-by-row basis. Once that is found, we are good to go on adjusting the focus.
  3. For the low-resolution, its easier. Simply move the focus to the middle of the screen by adjusting the offset. Then, optimize the amplitude of the remote focusing to optimize the sparsity/resolution/DCT.
  4. For the high-resolution, its harder. Would need to perform a 2D search for amplitude and offset to optimize the sparsity/resolution/DCT.
  5. And all of this should be done in a way that is robust to the sample not being great there, or present at all.

AdvancedImagingUTSW avatar Jul 27 '22 01:07 AdvancedImagingUTSW

Partially addressed by #452.

zacsimile avatar Jul 21 '23 01:07 zacsimile