Open-source could finally get the world’s microscopes speaking the same language

Re:Open-source could finally get the world’s microscopes spe... by tomnicholas on Monday October 02, 2023 @12:54PM (#37740911)

> Each pixel? Why?

I use the Zarr format (for climate science data rather than microscope data), and I think this is just poor wording in the article. In the Zarr specification the metadata is stored separately from the actual chunks of compressed array data. So the metadata applies at the array level, not the pixel level.

> Wait - are there optical microscopes that can create 3D images?

I think so - they do it by scanning lots of images at different focal lengths to create a 3D section (I think?). There are whole projects just for visualizing the multi-TeraByte 3D image files produced - Napari is an open-source image viewer which opens OME-Zarr data.

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Re:Open-source could finally get the world’s microscopes spe... by carreau on Monday October 02, 2023 @01:00PM (#37741014)

Even on classical 2D microscope the illumination can be non-uniform, and you might need to calibrate your image.

Source: PhD in biolab with microscopes, and napari dev.

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Re:Open-source could finally get the world’s microscopes spe... by dekhn on Monday October 02, 2023 @01:08PM (#37741160)

OME-zarr doesn't really storage per-pixel illumination data. Instead, the illumination will typically be storaged as a per-2D-plane metadata.

Flat fields, dark fields, and light fields can all be stored but would be their own arrays (structure of arrays rather than array of structures).

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