Merge pull request #53 from will-moore/hierarchy_browser

Hierarchy browser
ome · Oct 22, 2024 · bc41e93 · bc41e93
2 parents 7afb8ac + 21f480f
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diff --git a/ome2024-ngff-challenge/index.html b/ome2024-ngff-challenge/index.html
@@ -1,6 +1,7 @@
 <!doctype html>
 <html lang="en">
   <head>
+    <link rel="icon" href="/favicon-16x16.png" />
     <meta charset="UTF-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>ome2024-ngff-challenge</title>

diff --git a/ome2024-ngff-challenge/package-lock.json b/ome2024-ngff-challenge/package-lock.json
diff --git a/ome2024-ngff-challenge/package.json b/ome2024-ngff-challenge/package.json
@@ -15,6 +15,7 @@
   },
   "dependencies": {
     "papaparse": "^5.4.1",
+    "svelte-tiny-virtual-list": "^2.1.2",
     "zarrita": "^0.4.0-next.15"
   }
 }
diff --git a/ome2024-ngff-challenge/public/favicon-16x16.png b/ome2024-ngff-challenge/public/favicon-16x16.png
diff --git a/ome2024-ngff-challenge/public/github-mark-white.svg b/ome2024-ngff-challenge/public/github-mark-white.svg
diff --git a/ome2024-ngff-challenge/public/nfdi4bioimage.png b/ome2024-ngff-challenge/public/nfdi4bioimage.png
diff --git a/ome2024-ngff-challenge/public/ome-logomark.svg b/ome2024-ngff-challenge/public/ome-logomark.svg
diff --git a/ome2024-ngff-challenge/public/selectCaret.svg b/ome2024-ngff-challenge/public/selectCaret.svg
diff --git a/ome2024-ngff-challenge/public/vizarr_logo.png b/ome2024-ngff-challenge/public/vizarr_logo.png
diff --git a/ome2024-ngff-challenge/src/About.svelte b/ome2024-ngff-challenge/src/About.svelte
@@ -0,0 +1,71 @@
+<div>
+  <h2>Introduction</h2>
+  <p>
+    The <a href="https://forum.image.sc/t/ome2024-ngff-challenge/97363">2024 OME-NGFF Challenge</a>
+    was conceived at the
+    <a href="https://www.openmicroscopy.org/events/ome-community-meeting-2024/">
+      OME Annual Community Meeting</a>
+    in Dundee in May 2024. The stated goals of Challenge were:
+  </p>
+
+  <ul>
+    <li>
+      Collect examples of OME-Zarr from multiple modalities, use cases, and
+      institutions, available from a single location.
+    </li>
+    <li>
+      Test the utility (and lack thereof) of existing OME-Zarr metadata and
+      image viewers.
+    </li>
+    <li>
+      Advance the adoption of the Zarr V3 specification, and also existing
+      OME-Zarr RFCs.
+    </li>
+  </ul>
+  <p>
+    The inspiration for the Challenge came from presentations at the OME Meeting
+    that demonstrated the level of adoption of OME-Zarr, but highlighted the
+    poor findability of the data.
+  </p>
+  <p>
+    Work on the challenge started in earnest in July 2024. All progress is
+    tracked in the <a href="https://github.com/ome/ome2024-ngff-challenge">ome2024-ngff-challenge</a>
+    repo. It was agreed that the results
+    of the OME-NGFF Challenge would be presented at the
+    <a href="https://globalbioimaging.org/exchange-of-experience/exchange-of-experience-ix">
+      2024 Global BioImaging Meeting</a>.
+  </p>
+
+  <h2>Process</h2>
+  <p>
+    The Challenge was run via a series of virtual meetings coordinated on the
+    Image.sc Forums, with all
+    <a href="https://hackmd.io/3emKqKQsT_2U35vLepzDEQ">notes and lists of participants</a>
+    available.
+  </p>
+
+  <h2>Results</h2>
+  <p>
+    At the outset, we weren’t sure how much OME-Zarr data was available, if it
+    could be converted to Zarr V3, or how many organisations would participate.
+    In the end, we have far exceeded our expectations, with more than 0.5 PByte
+    of OME-Zarr made available, across a wide range of modalities.
+  </p>
+  <p>
+    To make the assembly as accessible as possible, we built the the OME-NGFF
+    Challenge Viewer [URL?}, which incorporates a CSV with locations of
+    datasets, and connects datasets to the OME NGFF Validator, for metadata
+    validation and viewing.
+  </p>
+  <p>
+    Perhaps the most important outcome of the Challenge is the establishment of
+    a federated bioimage data system based on OME-Zarr. To our knowledge, this
+    is the largest federated bioimage data collection ever assembled.
+  </p>
+</div>
+
+<style>
+  div {
+    margin: 15px;
+  }
+</style>