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@tlambert03 tlambert03 commented Dec 2, 2025

import nd2

with nd2.ND2File('input.nd2') as f:
    f.to_ome_zarr('output.ome.zarr')

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codspeed-hq bot commented Dec 2, 2025

CodSpeed Performance Report

Merging #278 will not alter performance

Comparing export-ome-zarr (12f7c3a) with main (4b741a2)

Summary

✅ 13 untouched

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codecov bot commented Dec 2, 2025

Codecov Report

❌ Patch coverage is 96.61017% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 94.21%. Comparing base (ce489fc) to head (12f7c3a).
⚠️ Report is 1 commits behind head on main.

Files with missing lines Patch % Lines
src/nd2/_ome_zarr.py 96.61% 2 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #278      +/-   ##
==========================================
+ Coverage   94.12%   94.21%   +0.08%     
==========================================
  Files          20       22       +2     
  Lines        2451     2575     +124     
==========================================
+ Hits         2307     2426     +119     
- Misses        144      149       +5     

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tlambert03 commented Dec 3, 2025

tips for "guessing" plate specs from a non-JOBS nd2 file:

For the non-JOBS file (wellplate96_4_wells_without_jobs.nd):

Wells acquired: A01, A04, B04, C02

Evidence of being a 96-well plate (even without JOBS metadata):

  1. Position names: Well names follow standard 96-well format (A01-H12, 8 rows × 12 cols)
  2. 96 positions defined: All 96 well positions are defined in uLoopPars.Points
  3. Well spacing ~9000 µm: X spacing = 8963.1 µm, Y spacing = 9009.5 µm - matches
    standard 96-well plate (9mm center-to-center)

How to detect wellplate format programmatically:

  • Parse position names for row-column pattern (regex: [A-H]\d{1,2})
  • Count unique rows (A-H = 8) and columns (1-12 = 12)
  • Calculate spacing between positions to verify (~9mm for 96-well)

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2 participants