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Ngff tools table #139
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Ngff tools table #139
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628e8ef
Initial ngff-tools.md page
will-moore 62b5cb5
Simplify link
will-moore 6b66321
reformat html to fewer lines
will-moore 2580a2f
Add bioformats2raw row to table
will-moore fc3bc0d
Try table with different orientation
will-moore b8f4ae7
Fix table
will-moore 8325055
Update tables
will-moore 36f376d
Add itkwidgets and webknosses
will-moore 563d5b9
Add back URL (not s3) to last table
will-moore 512d2f7
Fix links
will-moore 577331a
Adding more features to last table
will-moore ec89a03
Add sample data column
will-moore cd77dd2
Add v0.4 axes
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Multi-C and Multi-T as separate rows on table
will-moore 3145685
Remove URL (not s3) row of table. Not needed
will-moore dd907b9
Add sample links for plate, bioformats2raw.layout and transforms
will-moore d56abf3
Fix y -> n for bioformats2raw.layout for napari
will-moore 4e4cae0
Remove markdown table and older html table
will-moore c092d8c
tweak features with v0.4 etc, fix y (scale) values
will-moore 2393e95
Test red X for no
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Add OMERO to table
will-moore 848e80d
reformat viewer type
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reformat coordinateTransforms
will-moore 0f74a61
Add versions for various tools
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Add sample image for scale not 2
will-moore 7b420a7
Split coordinateTransformations row in two
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Add z-downsample link to table
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add 'translate onto'
will-moore 6c390ad
Split multscales coordinateTransformations into 2 rows
will-moore 36de81c
links to v0.4 spec for multiscales and coordinateTransformations
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| # OME-NGFF tools | ||
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| Various tools are available for viewing and working with OME-NGFF data. | ||
| The following tables document which features of the OME-NGFF spec are supported by which tools. | ||
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| ## Viewers | ||
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| The following versions of each viewer were used in testing: | ||
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| - <a href="https://napari.org">napari</a> 0.4.16 with plugin <a href="https://github.com/ome/napari-ome-zarr/">napari-ome-zarr</a>0.5.2 and <a href="https://github.com/ome/ome-zarr-py/">ome-zarr</a>0.6.0. | ||
| - <a href="https://github.com/hms-dbmi/vizarr/">vizarr</a> using <a href="https://hms-dbmi.github.io/vizarr">current viewer</a> October 2022. Open via URL - see <a href="https://hms-dbmi.github.io/vizarr/?source=https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.3/idr0079A/9836998.zarr">example</a>. | ||
| - <a href="https://github.com/mobie/mobie-viewer-fiji/">MoBIE</a> plugin for ImageJ/Fiji. Open with `Plugins > BigDataViewer > OME-Zarr > Open OME-Zarr From...` | ||
| - <a href="https://itkwidgets.readthedocs.io/en/latest">itkwidgets</a>. Use in a python notebook, or open via URL: See <a href="https://kitware.github.io/itk-vtk-viewer/app/?rotate=false&fileToLoad=https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr">example</a>. | ||
| - <a href="https://webknossos.org">webKnossos</a> version 19988. | ||
| - <a href="https://www.openmicroscopy.org/omero/">OMERO</a> with BioFormats <a href="https://github.com/ome/ZarrReader">ZarrReader</a> 0.2.0. | ||
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| <table> | ||
| <thead> | ||
| <tr> | ||
| <th></th> | ||
| <th>Sample data</th> | ||
| <th>napari</th> | ||
| <th>vizarr</th> | ||
| <th>MoBIE</th> | ||
| <th>itkwidgets</th> | ||
| <th>webKnossos</th> | ||
| <th>OMERO</th> | ||
| </tr> | ||
| </thead> | ||
| <tbody> | ||
| <tr> | ||
| <td>Viewer type, language</td> | ||
| <td></td> | ||
| <td>desktop, Python</td> | ||
| <td>browser, JavaScript</td> | ||
| <td>desktop, Java</td> | ||
| <td>notebook, Python</td> | ||
| <td>browser client + server</td> | ||
| <td>various clients + server</td> | ||
| </tr> | ||
| <tr> | ||
| <td>Z-downsampling</td> | ||
| <td></td> | ||
| <td>y</td> | ||
| <td><a href="https://github.com/hms-dbmi/vizarr/pull/71">n</a></td> | ||
| <td>y</td> | ||
| <td>y</td> | ||
| <td>y</td> | ||
| <td>n</td> | ||
| </tr> | ||
| <tr> | ||
| <td>omero info</td> | ||
| <td><a href="https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr">6001240.zarr</a></td> | ||
| <td>y</td> | ||
| <td>y</td> | ||
| <td>n</td> | ||
| <td><a href="https://github.com/InsightSoftwareConsortium/itkwidgets/issues/546">n</a></td> | ||
| <td>n</td> | ||
| <td>n?</td> | ||
| </tr> | ||
| <tr> | ||
| <td>multiscales factor not=2</td> | ||
| <td><a href="https://minio-dev.openmicroscopy.org/idr/v0.4/idr0082/9846318.zarr/0">9846318.zarr/0</a></td> | ||
| <td>y</td> | ||
| <td><a href="https://github.com/hms-dbmi/vizarr/issues/101">n</a></td> | ||
| <td>y</td> | ||
| <td>y</td> | ||
| <td>y</td> | ||
| <td>y?</td> | ||
| </tr> | ||
| <tr> | ||
| <td>axes (v0.3)</td> | ||
| <td><a href="https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.3/idr0079A/9836998.zarr">9836998.zarr</a></td> | ||
| <td>y</td> | ||
| <td>y</td> | ||
| <td>y</td> | ||
| <td>y</td> | ||
| <td>n</td> | ||
| <td>?</td> | ||
| </tr> | ||
| <tr> | ||
| <td>v0.4 axes (v0.4)</td> | ||
| <td><a href="https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0101A/13457227.zarr">13457227.zarr</a></td> | ||
| <td>y</td> | ||
| <td>y</td> | ||
| <td>y</td> | ||
| <td>y</td> | ||
| <td>y</td> | ||
| <td>?</td> | ||
| </tr> | ||
| <tr> | ||
| <td>3D view</td> | ||
| <td><a href="https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr">6001240.zarr</a></td> | ||
| <td>y (1)</td> | ||
| <td>n</td> | ||
| <td>y</td> | ||
| <td>y</td> | ||
| <td>y</td> | ||
| <td>n</td> | ||
| </tr> | ||
| <tr> | ||
| <td>labels</td> | ||
| <td><a href="https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0052A/5514375.zarr">5514375.zarr</a></td> | ||
| <td>y</td> | ||
| <td>n</td> | ||
| <td>y</td> | ||
| <td><a href="https://github.com/InsightSoftwareConsortium/itkwidgets/issues/547">n</a></td> | ||
| <td>y</td> | ||
| <td>?</td> | ||
| </tr> | ||
| <tr> | ||
| <td>HCS plate</td> | ||
| <td><a href="https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0001A/2551.zarr">idr0001</a></td> | ||
| <td>y</td> | ||
| <td>y</td> | ||
| <td>n</td> | ||
| <td>n</td> | ||
| <td>n</td> | ||
| <td>y</td> | ||
| </tr> | ||
| <tr> | ||
| <td>bioformats2raw.layout</td> | ||
| <td><a href="https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.2/idr0070A/9838562.zarr">9838562.zarr</a></td> | ||
| <td><a href="https://github.com/ome/napari-ome-zarr/issues/71">n</a></td> | ||
| <td><a href="https://github.com/hms-dbmi/vizarr/issues/149">n</a></td> | ||
| <td><span style="color: red">X</span></td> | ||
| <td>n</td> | ||
| <td>n</td> | ||
| <td>y</td> | ||
| </tr> | ||
| <tr> | ||
| <td>multiple 'multiscales'</td> | ||
| <td></td> | ||
| <td>n</td> | ||
| <td>n</td> | ||
| <td>n</td> | ||
| <td>n</td> | ||
| <td>n</td> | ||
| <td>n</td> | ||
| </tr> | ||
| <tr> | ||
| <td>datasets coordinateTransformations (v0.4)</td> | ||
| <td><a href="https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0101A/13457537.zarr">13457537.zarr</a> | ||
| translate onto <a href="https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0101A/13457227.zarr">13457227.zarr</a></td> | ||
| <td>y (scale, translate)</td> | ||
| <td>n</td> | ||
| <td>?</td> | ||
| <td>y (scale)</td> | ||
| <td>y (scale)</td> | ||
| <td>?</td> | ||
| </tr> | ||
| <tr> | ||
| <td>multiscales coordinateTransformations (v0.4)</td> | ||
| <td><a href="https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0101A/13457539.zarr">13457539.zarr</a></td> | ||
| <td>n</td> | ||
| <td>n</td> | ||
| <td>?</td> | ||
| <td>?</td> | ||
| <td>?</td> | ||
| <td>?</td> | ||
| </tr> | ||
| <tr> | ||
| <td>overlay multiple images</td> | ||
| <td></td> | ||
| <td>y</td> | ||
| <td>n</td> | ||
| <td>?</td> | ||
| <td>?</td> | ||
| <td>y</td> | ||
| <td>n</td> | ||
| </tr> | ||
| <tr> | ||
| <td>multiple Channels</td> | ||
| <td><a href="https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0101A/13457227.zarr">13457227.zarr</a></td> | ||
| <td>y</td> | ||
| <td>y</td> | ||
| <td>y</td> | ||
| <td>n</td> | ||
| <td>y</td> | ||
| <td>y</td> | ||
| </tr> | ||
| <tr> | ||
| <td>multiple Time-points</td> | ||
| <td><a href="https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0101A/13457227.zarr">13457227.zarr</a></td> | ||
| <td>y</td> | ||
| <td>y</td> | ||
| <td>y</td> | ||
| <td>n</td> | ||
| <td>n</td> | ||
| <td>y</td> | ||
| </tr> | ||
| </tbody> | ||
| </table> | ||
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| 1. napari 3D view only supported for lowest level of multiscales pyramid | ||
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This line, which says
webknossos opens ?should say something likeThis invites a split of this line into the first image (scale & transform) and the second image (scale).
We also need a better expression for the
nwhich at present means "does not support the feature which the particular image is trying to highlight, it opens the image but ignores the feature".