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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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Abort stalled acquisitions #81

Closed ieivanov closed 1 year ago

ieivanov commented 1 year ago

Issue #26 is not completely gone and the Oryx camera will every now and then drop a frame (once in a 8-hour acquisition?), leading to #41. In this PR I abort CZYX acquisitions which are taking too long such that we can proceed with the next timepoint. Tested and works well, ready to merge.

With the new version of pycromanager I observed no slowdown in a 3 hour acquisition, which was the original motivation for #22.

Separately, I'll look into why the camera may be dropping frames as outlined in #26 to get to the source of the issue.

Fixes https://github.com/czbiohub-sf/mantis/issues/64, https://github.com/czbiohub-sf/mantis/issues/41

Requires AcqEngJ 0.30.1 which, for now, I compile manually.

ieivanov commented 1 year ago

@talonchandler @edyoshikun can I get an approval for this PR?