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Merged
will-moore merged 3 commits into from
Jun 22, 2026
Merged

Website updates for zarr #221

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baa5416
about/index.html fixes
will-moore Jun 8, 2026
0bc58e6
Updates to submission page
will-moore Jun 8, 2026
f0e36a4
Merge remote-tracking branch 'origin/master' into website_updates_for…
will-moore Jun 15, 2026
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4 changes: 2 additions & 2 deletions index.html
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Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ <h2>Goal</h2>

<p>IDR datasets are annotated with author-supplied metadata (e.g., annotations, defined regions, feature vectors
and ontological annotations) that are all stored and available for browsing. All metadata are also available
through the <a href="https://www.openmicroscopy.org/site/support/omero5.2/developers/Modules/Api.html">OMERO API</a>.
through the <a href="api.html">JSON API</a>.

@dominikl dominikl Jun 9, 2026

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Doesn't this have to be about/api.html ?

@will-moore will-moore Jun 9, 2026

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I was looking at the following sentence which has <a href="submission.html">our submission guidelines</a> and that seems to work fine. They're just relative links to sibling pages.


<p>If you are interested in submitting data to the IDR, see <a href="submission.html">our submission guidelines</a>.</p>
</div>
Expand Down Expand Up @@ -78,7 +78,7 @@ <h2>Examples</h2>
<img class="thumbnail" alt="idr0007-A" src="https://idr.openmicroscopy.org/webgateway/render_thumbnail/95543/192/">
</a></div>
<div class="column"><a href="https://idr.openmicroscopy.org/webclient/?show=image-1230008" target="_blank">
<img class="thumbnail" src="https://idr.openmicroscopy.org/webgateway/render_thumbnail/1230008/192/" alt="idr-0001-A">
<img class="thumbnail" src="https://idr.openmicroscopy.org/webgateway/render_thumbnail/1230008/" alt="idr-0001-A">
</a></div>
<div class="column"><a href="https://idr.openmicroscopy.org/webclient/?show=image-1484759" target="_blank">
<img class="thumbnail" src="https://idr.openmicroscopy.org/webgateway/render_thumbnail/1484759/192/" alt="idr-0013-A">
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48 changes: 32 additions & 16 deletions submission.html
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Expand Up @@ -65,6 +65,33 @@ <h2>What we are looking for</h2>
</div>
<!-- end guidelines section -->

<!-- begin size section -->
<hr class="whitespace">
<div class="row column text-center">
<h2>Image data format: OME-Zarr</h2>
</div>
<hr>
<div class="row">
<div class="small-10 small-centered medium-10 medium-centered columns">
<div class="row horizontal">
<div>
<p>
The IDR accepts image data in <a href="https://ngff.openmicroscopy.org/">OME-Zarr</a> format.
A <a href="https://ngff.openmicroscopy.org/resources/tools/index.html#zarr-converters">number of tools</a>
are available for converting your image data into OME-Zarr format, including
the <a href="https://www.glencoesoftware.com/products/ngff-converter/">NGFF Converter</a>
desktop appliation.
</p>
<p>
If you have not yet converted your image data into OME-Zarr, please convert a small sample
and send it to us for testing. We can provide feedback on the conversion and help you with any issues.
</p>
</div>
</div>
</div>
</div>
<!-- end size section -->

<!-- begin size section -->
<hr class="whitespace">
<div class="row column text-center">
Expand Down Expand Up @@ -202,22 +229,11 @@ <h2>How to transfer images and metadata</h2>
<div class="small-10 small-centered medium-10 medium-centered columns">
<div class="row horizontal">
<div>
<p>There are several options for having your image data transferred to the IDR:
<ul>
<li><b>Provide a link</b>: if your data is already
available online (e.g. Dropbox, FTP, etc), a link to the location may be the
easiest option.</li>
<li><b>FTP</b>: data can be uploaded using our FTP
server. We will provide you with details via email.</li>
<li><b>Shipping disks</b>: Sending hard-drives by mail
remains a reliable way of transferring your data. We will provide you with
shipping details via email.</li>
<li><b>FTP / Aspera</b>: we are working on a link
between IDR and BioStudies (<a href="https://www.ebi.ac.uk/biostudies/submit">
https://www.ebi.ac.uk/biostudies/submit.html</a>). If
you can upload your image data to BioStudies via FTP or Aspera, IDR may be able
to access your data directly from there.</li>

<p>
OME-Zarr image data must be hosted on public object storage.
Please contact us at <a href="mailto:idr@openmicroscopy.org">idr@openmicroscopy.org</a>
to discuss options for hosting your data.
</p>
</div>
</div>
</div>
Expand Down