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ome / omero-figure

An OMERO.web app for creating Figures from images in OMERO
http://figure.openmicroscopy.org
GNU Affero General Public License v3.0
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Orthogonal projections. #353

Open iandobbie opened 4 years ago

iandobbie commented 4 years ago

Is there any way to get an orthogonal project into an figure without exporting the data, rotating in say FiJi around the relevant axis and then reimporting? As omero figure already does z-projections this is just going to be a similar extraction of data from the full 3D image, but then presenting it slightly differently.

will-moore commented 4 years ago

This has been requested elsewhere: see https://trello.com/c/VdL7RcAz/96-orthoganal-view

Unfortunately the orthogonal projection isn't provided by the OMERO.server rendering engine yet (https://docs.openmicroscopy.org/omero-blitz/5.5.3/slice2html/omero/api/RenderingEngine.html) (although you can get raw pixel data for any cube using getHyperCube (https://docs.openmicroscopy.org/omero-blitz/5.5.3/slice2html/omero/api/RawPixelsStore.html#getHypercube).

The only workaround I could think of is to create a new Image in OMERO that is an orthogonal view of an existing one, using a script similar to the Channel Offsets (https://github.com/ome/omero-scripts/blob/develop/omero/util_scripts/Channel_Offsets.py) This would duplicate the pixel data and have to be done before you start creating a Figure, but if you think that is a viable option then let us know.

Will

will-moore commented 1 year ago

Orthogonal view requested again on recent US trip. cc @jburel

jburel commented 1 year ago

The rendering engine offers the option to specify the plane to render. The default is XY