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chore(rebuild): Merge pull request #34 from constantinpape/main
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Add link to the ngff site to README.md

SHA: f8254d8
Reason: push, by @joshmoore

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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joshmoore and github-actions[bot] committed Feb 28, 2021
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36 changes: 18 additions & 18 deletions 0.1/index.html
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}
}
</style>
<meta content="Bikeshed version c5172e83, updated Fri Nov 20 15:35:20 2020 -0800" name="generator">
<meta content="Bikeshed version b94c7e755, updated Fri Feb 19 16:28:59 2021 -0800" name="generator">
<link href="https://ngff.openmicroscopy.org/0.1/" rel="canonical">
<meta content="f0046874b8bd74cfa8ebd4172a0e9ced00661f14" name="document-revision">
<meta content="f8254d8d2739a08e7973a3a20af212b9fbff6d5e" name="document-revision">
<style>/* style-autolinks */

.css.css, .property.property, .descriptor.descriptor {
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<div class="head">
<img alt="OME logo (6 circles in a hexagon)" src="http://www.openmicroscopy.org/img/logos/ome-logomark.svg" style="float:right;width:42px;height:42px;">
<h1 class="p-name no-ref" id="title">Next-generation file formats (NGFF)</h1>
<h2 class="no-num no-toc no-ref heading settled" id="subtitle"><span class="content">Final Community Group Report, <time class="dt-updated" datetime="2020-11-30">30 November 2020</time></span></h2>
<h2 class="no-num no-toc no-ref heading settled" id="subtitle"><span class="content">Final Community Group Report, <time class="dt-updated" datetime="2021-02-28">28 February 2021</time></span></h2>
<div data-fill-with="spec-metadata">
<dl>
<dt>This version:
Expand All @@ -1826,7 +1826,7 @@ <h2 class="no-num no-toc no-ref heading settled" id="subtitle"><span class="cont
</dl>
</div>
<div data-fill-with="warning"></div>
<p class="copyright" data-fill-with="copyright">Copyright © 2020 <a href="https://www.openmicroscopy.org/"><abbr title="Open Microscopy Environment">OME</abbr></a><sup>®</sup> (<a href="https://dundee.ac.uk/"><abbr title="University of Dundee">U. Dundee</abbr></a>).
<p class="copyright" data-fill-with="copyright">Copyright © 2021 <a href="https://www.openmicroscopy.org/"><abbr title="Open Microscopy Environment">OME</abbr></a><sup>®</sup> (<a href="https://dundee.ac.uk/"><abbr title="University of Dundee">U. Dundee</abbr></a>).
OME trademark rules apply. </p>
<hr title="Separator for header">
</div>
Expand Down Expand Up @@ -2059,10 +2059,10 @@ <h3 class="heading settled" data-level="3.1" id="multiscale-md"><span class="sec
<h3 class="heading settled" data-level="3.2" id="omero-md"><span class="secno">3.2. </span><span class="content">"omero" metadata</span><a class="self-link" href="#omero-md"></a></h3>
<p>Information specific to the channels of an image and how to render it
can be found under the "omero" key in the group-level metadata:</p>
<pre class="language-json highlight"><c- u>"id"</c->: <c- mi>1</c->, # ID in OMERO
<c- u>"name"</c->: <c- u>"example.tif"</c->, # Name as shown in the UI
<c- u>"version"</c->: <c- u>"0.1"</c->, # Current version
<c- u>"channels"</c->: <c- p>[</c-> # Array matching the c dimension size
<pre class="language-json highlight"><c- f>"id"</c-><c- p>:</c-> <c- mi>1</c-><c- p>,</c-> # ID i<c- kc>n</c-> OMERO
<c- f>"name"</c-><c- p>:</c-> <c- u>"example.tif"</c-><c- p>,</c-> # Name as show<c- kc>n</c-> i<c- kc>n</c-> <c- kc>t</c->he UI
<c- f>"version"</c-><c- p>:</c-> <c- u>"0.1"</c-><c- p>,</c-> # Curre<c- kc>nt</c-> versio<c- kc>n</c->
<c- f>"channels"</c-><c- p>:</c-> <c- p>[</c-> # Array ma<c- kc>t</c->chi<c- kc>n</c->g <c- kc>t</c->he c dime<c- kc>ns</c->io<c- kc>n</c-> size
<c- p>{</c->
<c- f>"active"</c-><c- p>:</c-> <c- kc>true</c-><c- p>,</c->
<c- f>"coefficient"</c-><c- p>:</c-> <c- mi>1</c-><c- p>,</c->
Expand All @@ -2077,10 +2077,10 @@ <h3 class="heading settled" data-level="3.2" id="omero-md"><span class="secno">3
<c- f>"start"</c-><c- p>:</c-> <c- mi>0</c->
<c- p>}</c->
<c- p>}</c->
<c- p>]</c->,
<c- u>"rdefs"</c->: <c- p>{</c->
<c- f>"defaultT"</c-><c- p>:</c-> <c- mi>0</c-><c- p>,</c-> # First timepoint to show the user
<c- f>"defaultZ"</c-><c- p>:</c-> <c- mi>118</c-><c- p>,</c-> # First Z section to show the user
<c- p>],</c->
<c- f>"rdefs"</c-><c- p>:</c-> <c- p>{</c->
<c- f>"defaultT"</c-><c- p>:</c-> <c- mi>0</c-><c- p>,</c-> # Firs<c- kc>t</c-> <c- kc>t</c->imepoi<c- kc>nt</c-> <c- kc>t</c->o show <c- kc>t</c->he user
<c- f>"defaultZ"</c-><c- p>:</c-> <c- mi>118</c-><c- p>,</c-> # Firs<c- kc>t</c-> Z sec<c- kc>t</c->io<c- kc>n</c-> <c- kc>t</c->o show <c- kc>t</c->he user
<c- f>"model"</c-><c- p>:</c-> <c- u>"color"</c-> # <c- u>"color"</c-> or <c- u>"greyscale"</c->
<c- p>}</c->
</pre>
Expand Down Expand Up @@ -2111,7 +2111,7 @@ <h3 class="heading settled" data-level="3.4" id="label-md"><span class="secno">3
image the label is associated with. If included it MAY include a key <code>image</code> whose value is the relative path to a Zarr image group. The default value is
"../../" since most labels are stored under a subgroup named "labels/" (see
above).</p>
<pre class="language-json highlight"><c- u>"image-label"</c->:
<pre class="language-json highlight"><c- f>"image-label"</c-><c- p>:</c->
<c- p>{</c->
<c- f>"version"</c-><c- p>:</c-> <c- u>"0.1"</c-><c- p>,</c->
<c- f>"colors"</c-><c- p>:</c-> <c- p>[</c->
Expand All @@ -2125,11 +2125,11 @@ <h3 class="heading settled" data-level="3.4" id="label-md"><span class="secno">3
<c- p>},</c->
...
<c- p>]</c->
<c- p>}</c->,
<c- u>"source"</c->: <c- p>{</c->
<c- p>},</c->
<c- f>"source"</c-><c- p>:</c-> <c- p>{</c->
<c- f>"image"</c-><c- p>:</c-> <c- u>"../../"</c->
<c- p>}</c->
]
<c- p>]</c->
</pre>
<h3 class="heading settled" data-level="3.5" id="plate-md"><span class="secno">3.5. </span><span class="content">"plate" metadata</span><a class="self-link" href="#plate-md"></a></h3>
<p>For high-content screening datasets, the plate layout can be found under the
Expand Down Expand Up @@ -2169,7 +2169,7 @@ <h3 class="heading settled" data-level="3.5" id="plate-md"><span class="secno">3
</dl>
<p>For example the following JSON object defines a plate with two acquisition and
6 wells (2 rows and 3 columns), containing up 2 fields of view per acquistion.</p>
<pre class="language-json highlight"><c- u>"plate"</c->: <c- p>{</c->
<pre class="language-json highlight"><c- f>"plate"</c-><c- p>:</c-> <c- p>{</c->
<c- f>"acquisitions"</c-><c- p>:</c-> <c- p>[</c->
<c- p>{</c->
<c- f>"id"</c-><c- p>:</c-> <c- mi>1</c-><c- p>,</c->
Expand Down Expand Up @@ -2246,7 +2246,7 @@ <h3 class="heading settled" data-level="3.6" id="well-md"><span class="secno">3.
<p>For example the following JSON object defines a well with four fields of
views. The first two fields of view were part of the first acquisition while
the last two fields of view were part of the second acquisition.</p>
<pre class="language-json highlight"><c- u>"well"</c->: <c- p>{</c->
<pre class="language-json highlight"><c- f>"well"</c-><c- p>:</c-> <c- p>{</c->
<c- f>"images"</c-><c- p>:</c-> <c- p>[</c->
<c- p>{</c->
<c- f>"acquisition"</c-><c- p>:</c-> <c- mi>1</c-><c- p>,</c->
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36 changes: 18 additions & 18 deletions latest/index.html
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Original file line number Diff line number Diff line change
Expand Up @@ -1484,9 +1484,9 @@
}
}
</style>
<meta content="Bikeshed version c5172e83, updated Fri Nov 20 15:35:20 2020 -0800" name="generator">
<meta content="Bikeshed version b94c7e755, updated Fri Feb 19 16:28:59 2021 -0800" name="generator">
<link href="https://ngff.openmicroscopy.org/latest/" rel="canonical">
<meta content="f0046874b8bd74cfa8ebd4172a0e9ced00661f14" name="document-revision">
<meta content="f8254d8d2739a08e7973a3a20af212b9fbff6d5e" name="document-revision">
<style>/* style-autolinks */

.css.css, .property.property, .descriptor.descriptor {
Expand Down Expand Up @@ -1812,7 +1812,7 @@
<div class="head">
<img alt="OME logo (6 circles in a hexagon)" src="http://www.openmicroscopy.org/img/logos/ome-logomark.svg" style="float:right;width:42px;height:42px;">
<h1 class="p-name no-ref" id="title">Next-generation file formats (NGFF)</h1>
<h2 class="no-num no-toc no-ref heading settled" id="subtitle"><span class="content">Editor’s Draft, <time class="dt-updated" datetime="2020-11-30">30 November 2020</time></span></h2>
<h2 class="no-num no-toc no-ref heading settled" id="subtitle"><span class="content">Editor’s Draft, <time class="dt-updated" datetime="2021-02-28">28 February 2021</time></span></h2>
<div data-fill-with="spec-metadata">
<dl>
<dt>This version:
Expand All @@ -1826,7 +1826,7 @@ <h2 class="no-num no-toc no-ref heading settled" id="subtitle"><span class="cont
</dl>
</div>
<div data-fill-with="warning"></div>
<p class="copyright" data-fill-with="copyright">Copyright © 2020 <a href="https://www.openmicroscopy.org/"><abbr title="Open Microscopy Environment">OME</abbr></a><sup>®</sup> (<a href="https://dundee.ac.uk/"><abbr title="University of Dundee">U. Dundee</abbr></a>).
<p class="copyright" data-fill-with="copyright">Copyright © 2021 <a href="https://www.openmicroscopy.org/"><abbr title="Open Microscopy Environment">OME</abbr></a><sup>®</sup> (<a href="https://dundee.ac.uk/"><abbr title="University of Dundee">U. Dundee</abbr></a>).
OME trademark rules apply. </p>
<hr title="Separator for header">
</div>
Expand Down Expand Up @@ -2058,10 +2058,10 @@ <h3 class="heading settled" data-level="3.1" id="multiscale-md"><span class="sec
<h3 class="heading settled" data-level="3.2" id="omero-md"><span class="secno">3.2. </span><span class="content">"omero" metadata</span><a class="self-link" href="#omero-md"></a></h3>
<p>Information specific to the channels of an image and how to render it
can be found under the "omero" key in the group-level metadata:</p>
<pre class="language-json highlight"><c- u>"id"</c->: <c- mi>1</c->, # ID in OMERO
<c- u>"name"</c->: <c- u>"example.tif"</c->, # Name as shown in the UI
<c- u>"version"</c->: <c- u>"0.1"</c->, # Current version
<c- u>"channels"</c->: <c- p>[</c-> # Array matching the c dimension size
<pre class="language-json highlight"><c- f>"id"</c-><c- p>:</c-> <c- mi>1</c-><c- p>,</c-> # ID i<c- kc>n</c-> OMERO
<c- f>"name"</c-><c- p>:</c-> <c- u>"example.tif"</c-><c- p>,</c-> # Name as show<c- kc>n</c-> i<c- kc>n</c-> <c- kc>t</c->he UI
<c- f>"version"</c-><c- p>:</c-> <c- u>"0.1"</c-><c- p>,</c-> # Curre<c- kc>nt</c-> versio<c- kc>n</c->
<c- f>"channels"</c-><c- p>:</c-> <c- p>[</c-> # Array ma<c- kc>t</c->chi<c- kc>n</c->g <c- kc>t</c->he c dime<c- kc>ns</c->io<c- kc>n</c-> size
<c- p>{</c->
<c- f>"active"</c-><c- p>:</c-> <c- kc>true</c-><c- p>,</c->
<c- f>"coefficient"</c-><c- p>:</c-> <c- mi>1</c-><c- p>,</c->
Expand All @@ -2076,10 +2076,10 @@ <h3 class="heading settled" data-level="3.2" id="omero-md"><span class="secno">3
<c- f>"start"</c-><c- p>:</c-> <c- mi>0</c->
<c- p>}</c->
<c- p>}</c->
<c- p>]</c->,
<c- u>"rdefs"</c->: <c- p>{</c->
<c- f>"defaultT"</c-><c- p>:</c-> <c- mi>0</c-><c- p>,</c-> # First timepoint to show the user
<c- f>"defaultZ"</c-><c- p>:</c-> <c- mi>118</c-><c- p>,</c-> # First Z section to show the user
<c- p>],</c->
<c- f>"rdefs"</c-><c- p>:</c-> <c- p>{</c->
<c- f>"defaultT"</c-><c- p>:</c-> <c- mi>0</c-><c- p>,</c-> # Firs<c- kc>t</c-> <c- kc>t</c->imepoi<c- kc>nt</c-> <c- kc>t</c->o show <c- kc>t</c->he user
<c- f>"defaultZ"</c-><c- p>:</c-> <c- mi>118</c-><c- p>,</c-> # Firs<c- kc>t</c-> Z sec<c- kc>t</c->io<c- kc>n</c-> <c- kc>t</c->o show <c- kc>t</c->he user
<c- f>"model"</c-><c- p>:</c-> <c- u>"color"</c-> # <c- u>"color"</c-> or <c- u>"greyscale"</c->
<c- p>}</c->
</pre>
Expand Down Expand Up @@ -2115,7 +2115,7 @@ <h3 class="heading settled" data-level="3.4" id="label-md"><span class="secno">3
image the label is associated with. If included it MAY include a key <code>image</code> whose value is the relative path to a Zarr image group. The default value is
"../../" since most labels are stored under a subgroup named "labels/" (see
above).</p>
<pre class="language-json highlight"><c- u>"image-label"</c->:
<pre class="language-json highlight"><c- f>"image-label"</c-><c- p>:</c->
<c- p>{</c->
<c- f>"version"</c-><c- p>:</c-> <c- u>"0.1"</c-><c- p>,</c->
<c- f>"colors"</c-><c- p>:</c-> <c- p>[</c->
Expand All @@ -2142,11 +2142,11 @@ <h3 class="heading settled" data-level="3.4" id="label-md"><span class="secno">3
<c- p>},</c->
...
<c- p>]</c->
<c- p>}</c->,
<c- u>"source"</c->: <c- p>{</c->
<c- p>},</c->
<c- f>"source"</c-><c- p>:</c-> <c- p>{</c->
<c- f>"image"</c-><c- p>:</c-> <c- u>"../../"</c->
<c- p>}</c->
]
<c- p>]</c->
</pre>
<h3 class="heading settled" data-level="3.5" id="plate-md"><span class="secno">3.5. </span><span class="content">"plate" metadata</span><a class="self-link" href="#plate-md"></a></h3>
<p>For high-content screening datasets, the plate layout can be found under the
Expand Down Expand Up @@ -2186,7 +2186,7 @@ <h3 class="heading settled" data-level="3.5" id="plate-md"><span class="secno">3
</dl>
<p>For example the following JSON object defines a plate with two acquisition and
6 wells (2 rows and 3 columns), containing up 2 fields of view per acquistion.</p>
<pre class="language-json highlight"><c- u>"plate"</c->: <c- p>{</c->
<pre class="language-json highlight"><c- f>"plate"</c-><c- p>:</c-> <c- p>{</c->
<c- f>"acquisitions"</c-><c- p>:</c-> <c- p>[</c->
<c- p>{</c->
<c- f>"id"</c-><c- p>:</c-> <c- mi>1</c-><c- p>,</c->
Expand Down Expand Up @@ -2263,7 +2263,7 @@ <h3 class="heading settled" data-level="3.6" id="well-md"><span class="secno">3.
<p>For example the following JSON object defines a well with four fields of
views. The first two fields of view were part of the first acquisition while
the last two fields of view were part of the second acquisition.</p>
<pre class="language-json highlight"><c- u>"well"</c->: <c- p>{</c->
<pre class="language-json highlight"><c- f>"well"</c-><c- p>:</c-> <c- p>{</c->
<c- f>"images"</c-><c- p>:</c-> <c- p>[</c->
<c- p>{</c->
<c- f>"acquisition"</c-><c- p>:</c-> <c- mi>1</c-><c- p>,</c->
Expand Down

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