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Support for light-sheet (meta) data #264

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constantinpape opened this issue Oct 9, 2024 · 0 comments
Open

Support for light-sheet (meta) data #264

constantinpape opened this issue Oct 9, 2024 · 0 comments

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@constantinpape
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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 ome/ome2024-ngff-challenge#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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