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czbiohub-sf / shrimPy

shrimPy: Smart High-throughput Robust Imaging & Measurement in Python
BSD 3-Clause "New" or "Revised" License
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mantis acquisitions save incorrect `z-step_um` metadata #58

Closed talonchandler closed 1 year ago

talonchandler commented 1 year ago

Mantis acquisitions save z-step_um = 0.01 (10 nm!?) to the micromanager metadata, which gets passed to the converted .zarr files.

@edyoshikun pointed me to the conversion factors that live in a comment in the acquisition .yml files:

z_step: 0.01  # 10 mV is equivalent to 310 nm

@edyoshikun also mentioned that he thinks this is a micromanager peculiarity wrt how we're driving the stage with a voltage.

Are there better ways handle this field? If we're stuck with passing voltages to z-step_um, then maybe we should pass the conversion factor as well?

This is not a blocker.

edyoshikun commented 1 year ago

tagging @ieivanov

ieivanov commented 1 year ago

There is a fix for this - currently we are using a DA Z Stage device adapter to covert between DAC voltage and stage position. The conversion factor is 1, such that 1V = 1 um. We can change that such that we use the correct scaling factor and then enter the scan parameters in um rather than voltage.

Will transfer this issue to the mantis repo.