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Standalone app#666

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will-moore wants to merge 58 commits intoome:masterfrom
will-moore:standalone_app
Open

Standalone app#666
will-moore wants to merge 58 commits intoome:masterfrom
will-moore:standalone_app

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@will-moore
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@will-moore will-moore commented Feb 2, 2026 •
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This was originally #619 before it got split into #663 with this one on top.

This branch is also pushed to master, so that it's deployed to https://will-moore.github.io/omero-figure/

Testing the standalone app:
Need to test all actions that load or save to OMERO

  • File > Open... Should ask for a local file OR a url to a file
    • The url should update to ?file=url so that refreshing will show the same file
  • File > Save (or Save button) should download the figure.json
  • Add Image - should only work for Zarr images
  • Export PDF should show a dialog (done) with info on how to export json to PDF as in Standalone python script #669 (not done yet)
  • Add Labels from Tags / KVP - either fail silently (same as in OMERO if no annotations) or hide/disable
  • Other options hidden (Delete, SetId)

@will-moore
First step - mostly add a zarr image
44e0e5d
@will-moore
Load all .zarray metadata. Convert pixelType
7ca2f61
@will-moore
npm install zarrita@next
746bcd3
@will-moore
Zarr rendering in panel_view.js
fc9fe8a
@will-moore
Simple caching of zarr stores and data
6b45fa2
@will-moore
Handle right panel setting of src async
3bbc15c
@will-moore
Handle async get_img_src() everywhere
4f53f7d
@will-moore
Add APP_SERVED_BY_OMERO global js variable
f9e76a7
@will-moore
Handle missing 'omero' metadata from zarr
f606f96
@will-moore
Update to use ome-zarr.js 0.0.6
f349124
@will-moore
Fix layout of multiple Zarr images when added together
a0da4ea
@will-moore
Fix render_scaled_region behaviour for BIG zarr images
f6a9df1
@will-moore
Fix saving of NGFF figures to OMERO
31352eb
@will-moore
isDark(color) handles invalid color
ae034d4
@will-moore
Fix bug in adding OMERO images
e3c969a
@will-moore
Remove baseUrl support in Open with. Zarrs links to ngff-validatator
5de8480
@will-moore
Handle 'scale' to populate pixel sizes
7a072de
@will-moore
Remove some console.log
a36d7d2
@will-moore
Fix LUT background on channel buttons and slider in OMERO
b9c1e21
@will-moore
Handle Zarr v3. ONLY save array.shape and array.dtype to figure JSON
f834d2b
@will-moore
Handle opening of OME-Zarr v0.3 images
39ab0b6
@will-moore
Fix Luts display, update zarrita and ome-zarr.js
ff86010
@will-moore
Remove APP_SERVED_BY_OMERO and Luts display logic
89c41f0
@will-moore
Remove unsupported importFromRemote() for adding public remote OMERO …
f6888ad 
…images
@will-moore
Handle zarr urls that end in /
d58c7a4
@will-moore
Info panel for zarr imagess shows URL instead of Image ID and Edit ID…
ea2eb45 
… button
@will-moore
Improve error handling when loading Zarr images
9f9c52d
@will-moore
Store zarr_version in figure.json
5974b66
@will-moore
Avoid duplicate loading of chunks when rendering
fd5121a 
When we adjusst rendering settings, right panel and figure panel both render at the same time. We don't
want to duplicate loading of chunks, so if the request is already pending, wait for it to complete the
use the cached value
@will-moore
Write OME-Zarr version to figure.json
4d16cab
@will-moore
Rename utils.getJson() to getJsonWithCredentials()
81d4a41
@will-moore
Use 'http' to identify zarr URLs rather than 'zarr'
7522bb4
@will-moore
Handle bf2raw, plate, CORS and File not found for Zarr
32b6c1b
@will-moore
boost targetSize for zarr rendering to 4 x size of panel
f012966
@will-moore
Use higher targetSize for non-big images
1a0bf21
@will-moore
Handle any missing values in omero.channels
03062bc
@will-moore
Revert "Remove APP_SERVED_BY_OMERO and Luts display logic"
2d70861 
This reverts commit 89c41f0.
@will-moore
Add gh-pages workflow to build and deploy
e04f3f2
@will-moore
Include .nojekyll in gh-pages deployment
85cbe85
@will-moore
Use ./ build path for gh-pages for ./assets as sibling to index.html
454e8b0
@will-moore
Support /figure/?file=http://url.figure.json
daa7e3b
@will-moore
Handle invalid file url
96841c8
@will-moore
Save if no OMERO downloads figure.json
f429237
@will-moore
vite.config.js base:'/figure/' to match gh-pages
2dff3bb
@will-moore
Update vite.config base:omero-figure
355cf52
@will-moore
File > Open loads from local. 'base' url is 'omero-figure'
eb0cb66 
To support deployment under /omero-figure/ on gh-pages
@will-moore
set unsaved:false on download
e626fd5
@will-moore
Hide omero-only UI elements, e.g. 'Delete' OR standalone UI elements
db92fa2
@will-moore
flake8 fix
3d30310
@will-moore will-moore marked this pull request as ready for review February 10, 2026 15:32
@snoopycrimecop
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snoopycrimecop commented Feb 23, 2026

Conflicting PR. Removed from build OMERO-plugins-push#67. See the console output for more details.
Possible conflicts:

--conflicts

@will-moore will-moore mentioned this pull request Feb 23, 2026
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snoopycrimecop commented Feb 26, 2026

Conflicting PR. Removed from build OMERO-plugins-push#70. See the console output for more details.
Possible conflicts:

--conflicts

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snoopycrimecop commented Feb 27, 2026

Conflicting PR. Removed from build OMERO-plugins-push#71. See the console output for more details.
Possible conflicts:

--conflicts

@snoopycrimecop snoopycrimecop mentioned this pull request Mar 4, 2026
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@will-moore @snoopycrimecop