Skip to content

Conversation

@ieivanov
Copy link
Contributor

No description provided.

@ziw-liu ziw-liu added the μManager Micro-Manager files and metadata label Jul 31, 2025
@ieivanov
Copy link
Contributor Author

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.

@ieivanov
Copy link
Contributor Author

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
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

μManager Micro-Manager files and metadata

Projects

None yet

Development

Successfully merging this pull request may close these issues.

capture the time interval between frames and units (min, second) in ome-zarr metadata

4 participants