ome / ome/ngff

Support for light-sheet (meta) data

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

Description

To support light sheet microscopy it would help to have a spec extension that can express typical metadata for LSM in a standardized way. Typically, LSMs record multiple image volumes that correspond to different image tiles, channels, illuminations, timepoints, etc. These are usually stored in an individual array due to serial acquisition and possible changes in dimensions (e.g. due to growth of the sample over time).

AFAIK the de-facto standard for this is using bdv.xml with additional attributes to describe tiles, channels etc. defined by BigSticher convention.
This format supports hdf5 or n5 to store the data.

Note: this issue was motivated by https://github.com/ome/ome2024-ngff-challenge/issues/49 and it makes sense to first wait on the release of the updated transformation spec #255 as this will be important to support here as well.

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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

Start by reading the updated transformation spec in issue #255 and the bdv.xml and BigStitcher conventions described here, including their HDF5 and N5 storage context. Define what the NGFF extension must standardize for tiles, channels, illuminations, timepoints, and independently stored image volumes; done means the proposed metadata model is specified and reviewed.

Written by the indexing model from the issue text.

Assessment

Tech stack
xml
Domain
data
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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