better autofocus support with MM for Z-stack

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better autofocus support with MM for Z-stack

cail
Dear All,

With 1.3.43a MM, if I want to run a time lapse imaging with autofocus (PFS) on and capturing Z-stack, I have to:

1. physically enable PFS, find the bottom of the focus plane
2. physically disable PFS (if PFS is on, the image plane will not change during the capture)
3. in Multi-D Acq window, enable autofocus/chosen PFS, use relative Z position, set the rage of 0 to 20 um (-10 to 10 um is not working if the autofocus is on, I don't know why)
4. set channels/time intervals ...

It would be really nice if MM could check the status of PFS before Multi-D Acq, disable it before the run and enable it after the run. I notice MM is checking PFS every frame during capture. However, if start the capture with PFS physically on, the Z position would not be able to change.

Thanks a lot.

Best,
Liang


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Re: better autofocus support with MM for Z-stack

Nico Stuurman-4
Hi Liang,

With 1.3.43a MM, if I want to run a time lapse imaging with autofocus (PFS) on and capturing Z-stack, I have to:

1. physically enable PFS, find the bottom of the focus plane
2. physically disable PFS (if PFS is on, the image plane will not change during the capture)
3. in Multi-D Acq window, enable autofocus/chosen PFS, use relative Z position, set the rage of 0 to 20 um (-10 to 10 um is not working if the autofocus is on, I don't know why)

Can you elaborate on "is not working"?  Does it take a z-stack, but not at the intended focal planes, or does something more spectacular bad happen?

It would be really nice if MM could check the status of PFS before Multi-D Acq, disable it before the run and enable it after the run. I notice MM is checking PFS every frame during capture. However, if start the capture with PFS physically on, the Z position would not be able to change.

This behavior is caused by the function "FullFocus" in the Nikon TI PSF adapter being very polite and not trying to double guess the user's intentions by leaving the PFS on if the user had it that way.  The problem with the solution that you propose is that people will want to run a full acquisition with the PFS on continuously.  I can imagine that it might work to switch off the PFS during acquisition if the user has chosen it to be the focus device.

Best,

Nico



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