Thickness of 2D slice
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- Dominant language
- Python
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Description
For some microscope modalities one collects 2D images, but it can make sense to still assign them a physical thickness along axis perpendicular to the 2D plane, e.g the axial extend of the PSF in light microscopy or the section thickness in TEM.
Such a thickness is interesting for analysis but also for rendering, e.g. when stacking many slices and then looking at them from the side.
How could we represent this in OME-Zarr? Would we store the data as 3D with the 3rd dimension having a length of one in dataspace?
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Research direction
Start by reviewing the OME-Zarr specification's existing conventions for 2D and 3D dataspace representations. Compare a singleton third dimension with a separate physical-thickness representation for analysis and side-view rendering. Done means the representation and its implications are agreed and documented.
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Assessment
- Domain
- data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100