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Compute time scale for ndtiff datasets#316

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Compute time scale for ndtiff datasets#316
ieivanov wants to merge 9 commits into
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feature/ndtiff_timescale

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ieivanov commented Sep 4, 2025

@srivarra could you please take this PR forward? The purpose is to include the correct time scale for NDTiff dataset, which is scraped from the acquisition metadata. We have a similar implementation for OME-Tiff datasets which was introduced here: #308. NDTiff datasets may not have perfectly uniform time sampling (say acquiring images at [0, 9.8, 10.2] seconds) so I introduced a linear fit to get the acquisition "rate". Frequently, we'll also skip acquiring a timepoint - for example if the autofocus has troubles engaging. In that case the next t_idx=3 will be skipped and t_idx will be written at ~40 seconds. My implementation may already work - please give it a try, I'll point you to a couple test datasets.

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ieivanov commented Sep 4, 2025

This dataset should be a good start: /hpc/instruments/cm.mantis/2025_02_28_A549_GOLGA2_DENV/2025_02_28_A549_GOLGA2_DENV_chunked_1/2025_02_28_A549_GOLGA2_DENV_chunked_labelfree_1/ Here the acquisition was aborted for 8 timepoints, you can check the acquisition logs for more info. The acquisition rate should come out to ~600 seconds per timepoint.

@ziw-liu ziw-liu added this to the 0.3.0 milestone Sep 5, 2025
@srivarra srivarra removed the μManager label Mar 2, 2026
srivarra added 4 commits March 3, 2026 13:01
Signed-off-by: Sricharan Reddy Varra <sricharan.varra@biohub.org>
Signed-off-by: Sricharan Reddy Varra <sricharan.varra@biohub.org>
Signed-off-by: Sricharan Reddy Varra <sricharan.varra@biohub.org>
@srivarra srivarra modified the milestones: 0.3.0, 0.3.1 Mar 25, 2026
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capture the time interval between frames and units (min, second) in ome-zarr metadata

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