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Show link to plate viewer on dataset page #553
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We should go with something like point 2: Drop the last 3 elements of the zarr_url Reason: The plate attribute is not actually enforced to be correctly matching the file name |
Example of image list
|
This looks like a great start for this feature! 👏🏻 Minor wording suggestion: |
I tested #562, and it works as expected. I imported this dataset {
"name": "test-2",
"zarr_dir": "/tmp/some/path/",
"images": [
{ "zarr_url": "/tmp/some/path/plate1/we/ll/a", "origin": null, "attributes": { "plate": "plate1" }, "types": {} },
{ "zarr_url": "/tmp/some/path/plate1/we/ll/b", "origin": null, "attributes": { "plate": "plate1" }, "types": {} },
{ "zarr_url": "/tmp/some/path/plate1/we/ll/c", "origin": null, "attributes": { "plate": "plate1" }, "types": {} },
{ "zarr_url": "/tmp/some/path/plate1/we/ll/d", "origin": null, "attributes": { "plate": "plate1" }, "types": {} },
{ "zarr_url": "/tmp/some/path/plate1/we/ll/e", "origin": null, "attributes": { "plate": "plate1" }, "types": {} },
{ "zarr_url": "/tmp/some/path/plate1/we/ll/f", "origin": null, "attributes": { "plate": "plate1" }, "types": {} },
{ "zarr_url": "/tmp/some/path/plate1/we/ll/g", "origin": null, "attributes": { "plate": "plate1" }, "types": {} },
{ "zarr_url": "/tmp/some/path/plate1/we/ll/h", "origin": null, "attributes": { "plate": "plate1" }, "types": {} },
{ "zarr_url": "/tmp/some/path/plate2/we/ll/a", "origin": null, "attributes": { "plate": "plate2" }, "types": {} },
{ "zarr_url": "/tmp/some/path/plate2/we/ll/b", "origin": null, "attributes": { "plate": "plate2" }, "types": {} },
{ "zarr_url": "/tmp/some/path/plate2/we/ll/c", "origin": null, "attributes": { "plate": "plate2" }, "types": {} },
{ "zarr_url": "/tmp/some/path/plate2/we/ll/d", "origin": null, "attributes": { "plate": "plate2" }, "types": {} },
{ "zarr_url": "/tmp/some/path/plate2/we/ll/e", "origin": null, "attributes": { "plate": "plate2" }, "types": {} },
{ "zarr_url": "/tmp/some/path/plate2/we/ll/f", "origin": null, "attributes": { "plate": "plate2" }, "types": {} },
{ "zarr_url": "/tmp/some/path/plate2/we/ll/g", "origin": null, "attributes": { "plate": "plate2" }, "types": {} },
{ "zarr_url": "/tmp/some/path/plate2/we/ll/h", "origin": null, "attributes": { "plate": "plate2" }, "types": {} },
{ "zarr_url": "/tmp/some/path/plate3/we/ll/a", "origin": null, "attributes": { "plate": "plate3" }, "types": {} },
{ "zarr_url": "/tmp/some/path/plate3/we/ll/b", "origin": null, "attributes": { "plate": "plate3" }, "types": {} },
{ "zarr_url": "/tmp/some/path/plate3/we/ll/c", "origin": null, "attributes": { "plate": "plate3" }, "types": {} },
{ "zarr_url": "/tmp/some/path/plate3/we/ll/d", "origin": null, "attributes": { "plate": "plate3" }, "types": {} },
{ "zarr_url": "/tmp/some/path/plate3/we/ll/e", "origin": null, "attributes": { "plate": "plate3" }, "types": {} },
{ "zarr_url": "/tmp/some/path/plate3/we/ll/f", "origin": null, "attributes": { "plate": "plate3" }, "types": {} },
{ "zarr_url": "/tmp/some/path/plate3/we/ll/g", "origin": null, "attributes": { "plate": "plate3" }, "types": {} },
{ "zarr_url": "/tmp/some/path/plate3/we/ll/h", "origin": null, "attributes": { "plate": "plate3" }, "types": {} }
],
"filters": {
"attributes": {},
"types": {}
}
} The "View" button of the first image points to http://localhost:3000/?source=http://localhost:3000/data/tmp/some/path/plate1/we/ll/a. I selected "plate2", and got |
The vizarr viewer links on the dataset page are very useful!
Currently, we only link to the individual images, e.g. the full zarr url. For example:
https://fractal.mls.uzh.ch/vizarr/?source=https://fractal.mls.uzh.ch/vizarr/data/data/active/jluethi/Fractal/20240723_23well_benchmark/20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr/B/03/0
A thing that is also super useful is linking to the plate view. By going to this url:
https://fractal.mls.uzh.ch/vizarr/?source=https://fractal.mls.uzh.ch/vizarr/data/data/active/jluethi/Fractal/20240723_23well_benchmark/20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr
(just removing the sub path to row, col & image)
We see:
We have metadata about whether a dataset has plates and what plates are available in the image list:
The goal would be that:
If there are plates in the image list
Show selector for which plate to load. And show a button for "view plate" that send the user to the link above.
This should be displayed above the image list for the moment. I may have additional ideas of where we expose this in the future :)
How do we get the plate url? I'd say we take the first zarr_url with the plate attribute. Given its zarr_url, we reconstruct the plate url. I see 2 ways:
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