czbiohub-sf / shrimPy

shrimPy: Smart High-throughput Robust Imaging & Measurement in Python
BSD 3-Clause "New" or "Revised" License
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realign LF remote refocus arm #23

Closed ieivanov closed 1 year ago

ieivanov commented 1 year ago

Alignment issues we have identified so far:

We need to identify a good time when to resolve these issues. This will likely require 3-5 days of downtime

ieivanov commented 1 year ago

We have planned to compare phase imaging on the Nikon side port (Epi camera) and the LF RR path (Oryx camera) with the benchmark target. If we see that phase imaging is not working as well in the LF RR path, it will be worth to fix all issues outlined above.

@edyoshikun to image the benchmark target, you'll need to place it in water - put a drop of water on a coverslip and place the target face down on the coverslip. This will reduce the phase delay of the target features, making them more comparable to biological samples. The target has features of varying phase density, try to pick the thinner, less phase dense features.