# Get Your Brain Together HCK 02: Anatomic orientation in OME-Zarr NGFF 2023-05-23 ## Attendees - Josh Moore, OME - David Feng, AIND - Sharmi, AIND - Nick TL, Vanderbilt - Nick Lusk, AIND - Lydia Ng, AIBS - Cai McCann, - Camilo Laiton - Alan Watson - Christian - Christian - Dzenan Zukic, Kitware - Beatriz, Cajal Neuro - Yael Balbastre - Alan Watson, U Pitt - Niles, Cajal Neuro - Satra G, MIT - Matt McCormick, Kitware ## Discussion ### *Standard, default orientation*? - LPS? - RAI? - RAS? * - [...] ### Where to store? - v0.5 later this summer - More Transformations - Add orientation to Transform Spec - https://github.com/ome/ngff/issues/84 - https://github.com/ome/ngff/pull/138#issuecomment-1467186626 - Let's merge Affine Transforms GitHub Flash Mob - @type - Scale - AnatomicalToRAS - Radial - captures more information not captured by current transformations - Death to ambiguity - Spatial Transcriptomics data storage - https://spatialdata.scverse.org/ - Add to data officially before v0.5 released - Propose incremental change to John's transformations proposal may be a good path forward - New specification - Lead authors connection with Josh M - `axes`, `long_name` - https://github.com/ome/ngff/issues/142 - `long_name` describes axis identifier, direction - Registration transformations - Space names - Many registration transformations that mapping to the same anatomic space - Define expectations - Where and how these are handled - Transformations that go beyond rough anatomical orientation go into separate Zarr paths / groups from the multiscale image group - Expected sequence or expected conventions for provenance of transformations - Do not have to re-write data associated with transformations - https://earthmover.io/ ### How to standardize? - Zarr spec? - No current mechanism - "multiscale" proposed, -> OME spec - Geo-Zarr now adding multiscales as "Zarr" - https://github.com/zarr-developers/geozarr-spec - Spatial concepts - May be difficult to converge with OME-Zarr - OME spec? - Pubish specification - Schema that can be validated ### How to encode? #### Terms relative to the body or the embryonic forebrain - https://www.quora.com/Can-you-tell-me-the-key-differences-between-anterior-versus-posterior-ventral-versus-dorsal-and-rostral-versus-caudal-in-terms-of-which-positions-they-are-referring-to-in-anatomical-terminology #### Direction matrix - Affine transformation - Rigid rotation (direction cosines) - Pre-concatenated (preferred), vs concatenated - Axis-aligned, human readable metadata - Nifti, ITK - Orientation matrix defines how to rotate into a prescribed orientation - S-form and Q-form - Has caused confusion - Scanner and RAS - and this is the set of nifti intent codes: https://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html/document_view Progression, named, concatenated transformation 1. Scale 2. Translation 3. Rough axis-aligned axes, (matrix of 1's, -1's and 0's ?) 4. Refined orientation / direction matrix #### Representation, e.g. "LPS", "left-posterior-superior", "left-to-right" - Towards - Nifti to and from discussion - https://docs.google.com/document/d/11gCzXOPUbYyuQx8fErtMO9tnOKC3kTWiL9axWkkILNE/edit#heading=h.mqkmyp254xh6 - some of it was later codified in nitransforms (a python library now): https://nitransforms.readthedocs.io/en/latest/notebooks/isbi2020.html - Be explicit - Bring bioimaging and biomedical communities together - Try to be inclusive - Enum - Controlled vocabulary - https://bids-specification.readthedocs.io/en/stable/appendices/coordinate-systems.html#image-based-coordinate-systems - Define translations as needed - Provenance - who defined the transform / coordinate system - can you have multiple? - are they overwritten? (no yes/no answer; all interpretation)