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Adjust README #72

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merged 3 commits into from
Nov 3, 2022
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Adjust README #72

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d5a14c3
Adjust README
pwalczysko Nov 3, 2022
509461c
Add flag cf. Will's comment
pwalczysko Nov 3, 2022
2680af2
Mention the flag, cf. Will's comment
pwalczysko Nov 3, 2022
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22 changes: 12 additions & 10 deletions README.md
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Expand Up @@ -24,35 +24,36 @@ https://napari.org/docs/plugins/index.html

## Installation

You can install `napari-ome-zarr` via [pip]:
[Install napari] if not already installed.

You can install `napari-ome-zarr` via [pip]. Activate the same environment as you installed napari into, then:

pip install napari-ome-zarr

## Usage

Napari will use `ome-zarr` to open images that the plugin recognises as ome-zarr.
Napari will use `napari-ome-zarr` plugin to open images that the plugin recognises as ome-zarr.
The image metadata from OMERO will be used to set channel names and rendering settings
in napari::

$ napari "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.3/9836842.zarr/"
napari "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.3/9836842.zarr/"


If a dialog in napari pops up, encouraging you to choose a reader, choose ``napari-ome-zarr`` and click OK.
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Could mention that you can specify the plugin on cli with napari --plugin napari-ome-zarr "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.3/9836842.zarr/"

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But, confusingly, when opening from S3, napari is not confused about which plugin to use.
Whereas locally, it is different, such as

napari --plugin napari-ome-zarr '6001240.zarr'

Does not produce a dialog, whereas

napari  '6001240.zarr'

Produces

Screenshot 2022-11-03 at 11 09 57

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fixed in 509461c

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I don't know why the difference when the file is local. But you say "If a dialog in napari pops up, encouraging you to choose a reader, choose napari-ome-zarr and click OK."
If that happens, you can stop it happening with --plugin napari-ome-zarr, regardless of whether the file is local or not. So I would mention --plugin napari-ome-zarr option before mentioning local usage

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fixed in 2680af2


# Also works with local files
$ napari 6001240.zarr
To open a local file::

napari 13457227.zarr

OR in python::

import napari

viewer = napari.Viewer()
viewer.open('https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.3/9836842.zarr/')
viewer.open("https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0101A/13457537.zarr", plugin="napari-ome-zarr")

napari.run()

If single zarray is passed to the plugin, it will be opened without the use of
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When I tried this, I didn't need the napari.run() at least in a python terminal

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Yes, can confirm this in python terminal. But if you leave it out in the script, then napari opens and immediately closes. With the napari.run() in the script, napari persists and is usable.

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Ah 👍

the metadata::

$ napari '/tmp/6001240.zarr/0'

## Contributing

Expand All @@ -68,6 +69,7 @@ Distributed under the terms of the [BSD-3] license,

If you encounter any problems, please [file an issue] along with a detailed description.

[Install napari]: https://napari.org/stable/tutorials/fundamentals/installation.html
[napari]: https://github.com/napari/napari
[Cookiecutter]: https://github.com/audreyr/cookiecutter
[@napari]: https://github.com/napari
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