ome / ome/ngff

units for data

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enhancement
Dominant language
Python
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171
Forks
75
Avg merge
2d 3h
Merged PRs (30d)
20

Description

The spec should express the units of the quantity represented in an image. This is a pretty important piece of metadata about an image; units are essential for interpreting images as the results of physical measurements / simulations.

Examples of images made of quantities with different units:

  • FLIM images might have intensities that represent time-binned photon counts, and processed FLIM images might have units like tau, which I think is a unitless quantity that represents the inferred exponential decay of fluorescence (someone who does FLIM should correct me if I'm getting something wrong here).
  • Fluorescent calcium imaging of active cells produces images where the intensities represent time-binned photon flux (or time-binned electrons flux, if you start at the camera chip), but these images are typically processed to produce images that represent % change over baseline, etc.

As a rough proposal, I would suggest that this metadata look something like this:

{
"units" : "W m-2",
"standard_name" : "irradiative flux",
"description" : "nice description of light getting collected",
}

One thing we could do with this metadata is go beyond physical units to express label / segmentation images:

{
"units" : "1",
"standard_name" : "instance_label",
"description" : "separate instances of a single semantic class.",
}

This would solve a problem for viewer software that need to know whether to open an image as a collection of intensities or as a collection of labels (e.g., napari's image layer vs label layer).

I'm not 100% sold on these examples, and I don't know where this metadata should live, but I think we should find some way to express this information. Thoughts?

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

The issue names no file, test, or entry point. Begin by locating the existing NGFF metadata and schema definitions, then review how image quantities and label or segmentation semantics are currently represented. Done requires an agreed metadata location and schema for units and image interpretation, rather than only the tentative examples in the issue.

Written by the indexing model from the issue text.

Assessment

Domain
data
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Quiet
Clarity
Needs clarification
Newbie friendliness
30/100

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