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chore(rebuild): Merge pull request #24 from melissalinkert/sparse-plate
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Clarify plate and well specifications for sparse plates

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Reason: push, by @sbesson

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<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="2022-01-27">27 January 2022</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="2022-02-02">2 February 2022</time></span></h2>
<div data-fill-with="spec-metadata">
<dl>
<dt>This version:
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<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="2022-01-27">27 January 2022</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="2022-02-02">2 February 2022</time></span></h2>
<div data-fill-with="spec-metadata">
<dl>
<dt>This version:
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<h1 class="p-name no-ref" id="title">Next-generation file formats (NGFF)</h1>
<p id="w3c-state"><a href="https://www.w3.org/standards/types#CG-FINAL">Final Community Group Report</a>, <time class="dt-updated" datetime="2022-01-27">27 January 2022</time></p>
<p id="w3c-state"><a href="https://www.w3.org/standards/types#CG-FINAL">Final Community Group Report</a>, <time class="dt-updated" datetime="2022-02-02">2 February 2022</time></p>
<details open>
<summary>More details about this document</summary>
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<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="2022-01-27">27 January 2022</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="2022-02-02">2 February 2022</time></span></h2>
<div data-fill-with="spec-metadata">
<dl>
<dt>This version:
Expand Down Expand Up @@ -2017,7 +2017,7 @@ <h3 class="heading settled" data-level="2.1" id="image-layout"><span class="secn
</pre>
<h3 class="heading settled" data-level="2.2" id="hcs-layout"><span class="secno">2.2. </span><span class="content">High-content screening</span><a class="self-link" href="#hcs-layout"></a></h3>
<p>The following specification defines the hierarchy for a high-content screening
dataset. Three groups must be defined above the images:</p>
dataset. Three groups MUST be defined above the images:</p>
<ul>
<li data-md>
<p>the group above the images defines the well and MUST implement the <a href="#well-md">well specification</a>. All images contained in a well are fields
Expand All @@ -2028,6 +2028,8 @@ <h3 class="heading settled" data-level="2.2" id="hcs-layout"><span class="secno"
<p>the group above the well row defines an entire plate i.e. a two-dimensional
collection of wells organized in rows and columns. It MUST implement the <a href="#plate-md">plate specification</a></p>
</ul>
<p>A well row group SHOULD NOT be present if there are no images in the well row.
A well group SHOULD NOT be present if there are no images in the well.</p>
<pre>. # Root folder, potentially in S3,
│
└── 5966.zarr # One plate (id=5966) converted to Zarr
Expand Down Expand Up @@ -2276,8 +2278,13 @@ <h3 class="heading settled" data-level="3.7" id="plate-md"><span class="secno">3
<dt><strong>columns</strong>
<dd>A list of JSON objects defining the columns of the plate. Each column
object defines the properties of the column at the index of the object
in the list. If not empty, it MUST contain a <code>name</code> key specifying the
column name.
in the list. Each column in the physical plate MUST be defined, even
if no wells in the column are defined. Each defined column MUST contain
a <code>name</code> key specifying the column name. The <code>name</code> MUST contain only
alphanumeric characters, MUST be case-sensitive, and MUST NOT be a
duplicate of any other <code>name</code> in the <code>columns</code> list. Care SHOULD be
taken to avoid collisions on case-insensitive filesystems
(e.g. avoid using both <code>Aa</code> and <code>aA</code>).
<dt><strong>field_count</strong>
<dd>An integer defining the maximum number of fields per view across all
wells.
Expand All @@ -2286,16 +2293,28 @@ <h3 class="heading settled" data-level="3.7" id="plate-md"><span class="secno">3
<dt><strong>rows</strong>
<dd>A list of JSON objects defining the rows of the plate. Each row object
defines the properties of the row at the index of the object in the
list. If not empty, it MUST contain a <code>name</code> key specifying the row
name.
list. Each row in the physical plate MUST be defined, even if no wells
in the row are defined. Each defined row MUST contain a <code>name</code> key
specifying the row name. The <code>name</code> MUST contain only alphanumeric
characters, MUST be case-sensitive, and MUST NOT be a duplicate
of any other <code>name</code> in the <code>rows</code> list. Care SHOULD be taken to avoid
collisions on case-insensitive filesystems (e.g. avoid using both <code>Aa</code> and <code>aA</code>).
<dt><strong>version</strong>
<dd>A string defining the version of the specification.
<dt><strong>wells</strong>
<dd>A list of JSON objects defining the wells of the plate. Each well object
MUST contain a <code>path</code> key identifying the path to the well subgroup.
The <code>path</code> MUST consist of a <code>name</code> in the <code>rows</code> list, a file separator (<code>/</code>),
and a <code>name</code> from the <code>columns</code> list, in that order. The <code>path</code> MUST NOT contain
additional leading or trailing directories.
Each well object MUST contain both a <code>rowIndex</code> key identifying the index into
the <code>rows</code> list and a <code>columnIndex</code> key indentifying the index into
the <code>columns</code> list. <code>rowIndex</code> and <code>columnIndex</code> MUST be 0-based.
The <code>rowIndex</code>, <code>columnIndex</code>, and <code>path</code> MUST all refer to the same
row/column pair.
</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>
<p>For example the following JSON object defines a plate with two acquisitions and
6 wells (2 rows and 3 columns), containing up to 2 fields of view per acquisition.</p>
<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->
Expand Down Expand Up @@ -2335,43 +2354,147 @@ <h3 class="heading settled" data-level="3.7" id="plate-md"><span class="secno">3
<c- f>"version"</c-><c- p>:</c-> <c- u>"0.3"</c-><c- p>,</c->
<c- f>"wells"</c-><c- p>:</c-> <c- p>[</c->
<c- p>{</c->
<c- f>"path"</c-><c- p>:</c-> <c- u>"2020-10-10/A/1"</c->
<c- f>"path"</c-><c- p>:</c-> <c- u>"A/1"</c-><c- p>,</c->
<c- f>"rowIndex"</c-><c- p>:</c-> <c- mi>0</c-><c- p>,</c->
<c- f>"columnIndex"</c-><c- p>:</c-> <c- mi>0</c->
<c- p>},</c->
<c- p>{</c->
<c- f>"path"</c-><c- p>:</c-> <c- u>"2020-10-10/A/2"</c->
<c- f>"path"</c-><c- p>:</c-> <c- f>"A/2"</c->
<c- f>"rowIndex"</c-><c- p>:</c-> <c- mi>0</c-><c- p>,</c->
<c- f>"columnIndex"</c-><c- p>:</c-> <c- mi>1</c->
<c- p>},</c->
<c- p>{</c->
<c- f>"path"</c-><c- p>:</c-> <c- u>"2020-10-10/A/3"</c->
<c- f>"path"</c-><c- p>:</c-> <c- f>"A/3"</c->
<c- f>"rowIndex"</c-><c- p>:</c-> <c- mi>0</c-><c- p>,</c->
<c- f>"columnIndex"</c-><c- p>:</c-> <c- mi>2</c->
<c- p>},</c->
<c- p>{</c->
<c- f>"path"</c-><c- p>:</c-> <c- u>"2020-10-10/B/1"</c->
<c- f>"path"</c-><c- p>:</c-> <c- f>"B/1"</c->
<c- f>"rowIndex"</c-><c- p>:</c-> <c- mi>1</c-><c- p>,</c->
<c- f>"columnIndex"</c-><c- p>:</c-> <c- mi>0</c->
<c- p>},</c->
<c- p>{</c->
<c- f>"path"</c-><c- p>:</c-> <c- u>"2020-10-10/B/2"</c->
<c- f>"path"</c-><c- p>:</c-> <c- f>"B/2"</c->
<c- f>"rowIndex"</c-><c- p>:</c-> <c- mi>1</c-><c- p>,</c->
<c- f>"columnIndex"</c-><c- p>:</c-> <c- mi>1</c->
<c- p>},</c->
<c- p>{</c->
<c- f>"path"</c-><c- p>:</c-> <c- u>"2020-10-10/B/3"</c->
<c- f>"path"</c-><c- p>:</c-> <c- f>"B/3"</c->
<c- f>"rowIndex"</c-><c- p>:</c-> <c- mi>1</c-><c- p>,</c->
<c- f>"columnIndex"</c-><c- p>:</c-> <c- mi>2</c->
<c- p>}</c->
<c- p>]</c->
<c- p>}</c->
</pre>
<p>The following JSON object defines a sparse plate with one acquisition and
2 wells in a 96 well plate, containing one field of view per acquisition.</p>
<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->
<c- f>"maximumfieldcount"</c-><c- p>:</c-> <c- mi>1</c-><c- p>,</c->
<c- f>"name"</c-><c- p>:</c-> <c- u>"single acquisition"</c-><c- p>,</c->
<c- f>"starttime"</c-><c- p>:</c-> <c- mi>1343731272000</c->
<c- p>},</c->
<c- p>],</c->
<c- f>"columns"</c-><c- p>:</c-> <c- p>[</c->
<c- p>{</c->
<c- f>"name"</c-><c- p>:</c-> <c- u>"1"</c->
<c- p>},</c->
<c- p>{</c->
<c- f>"name"</c-><c- p>:</c-> <c- u>"2"</c->
<c- p>},</c->
<c- p>{</c->
<c- f>"name"</c-><c- p>:</c-> <c- u>"3"</c->
<c- p>},</c->
<c- p>{</c->
<c- f>"name"</c-><c- p>:</c-> <c- u>"4"</c->
<c- p>},</c->
<c- p>{</c->
<c- f>"name"</c-><c- p>:</c-> <c- u>"5"</c->
<c- p>},</c->
<c- p>{</c->
<c- f>"name"</c-><c- p>:</c-> <c- u>"6"</c->
<c- p>},</c->
<c- p>{</c->
<c- f>"name"</c-><c- p>:</c-> <c- u>"7"</c->
<c- p>},</c->
<c- p>{</c->
<c- f>"name"</c-><c- p>:</c-> <c- u>"8"</c->
<c- p>},</c->
<c- p>{</c->
<c- f>"name"</c-><c- p>:</c-> <c- u>"9"</c->
<c- p>},</c->
<c- p>{</c->
<c- f>"name"</c-><c- p>:</c-> <c- u>"10"</c->
<c- p>},</c->
<c- p>{</c->
<c- f>"name"</c-><c- p>:</c-> <c- u>"11"</c->
<c- p>},</c->
<c- p>{</c->
<c- f>"name"</c-><c- p>:</c-> <c- u>"12"</c->
<c- p>}</c->
<c- p>],</c->
<c- f>"field_count"</c-><c- p>:</c-> <c- mi>1</c-><c- p>,</c->
<c- f>"name"</c-><c- p>:</c-> <c- u>"sparse test"</c-><c- p>,</c->
<c- f>"rows"</c-><c- p>:</c-> <c- p>[</c->
<c- p>{</c->
<c- f>"name"</c-><c- p>:</c-> <c- u>"A"</c->
<c- p>},</c->
<c- p>{</c->
<c- f>"name"</c-><c- p>:</c-> <c- u>"B"</c->
<c- p>},</c->
<c- p>{</c->
<c- f>"name"</c-><c- p>:</c-> <c- u>"C"</c->
<c- p>},</c->
<c- p>{</c->
<c- f>"name"</c-><c- p>:</c-> <c- u>"D"</c->
<c- p>},</c->
<c- p>{</c->
<c- f>"name"</c-><c- p>:</c-> <c- u>"E"</c->
<c- p>},</c->
<c- p>{</c->
<c- f>"name"</c-><c- p>:</c-> <c- u>"F"</c->
<c- p>},</c->
<c- p>{</c->
<c- f>"name"</c-><c- p>:</c-> <c- u>"G"</c->
<c- p>},</c->
<c- p>{</c->
<c- f>"name"</c-><c- p>:</c-> <c- u>"H"</c->
<c- p>}</c->
<c- p>],</c->
<c- f>"version"</c-><c- p>:</c-> <c- u>"0.1"</c-><c- p>,</c->
<c- f>"wells"</c-><c- p>:</c-> <c- p>[</c->
<c- p>{</c->
<c- f>"path"</c-><c- p>:</c-> <c- f>"C/5"</c->
<c- f>"rowIndex"</c-><c- p>:</c-> <c- mi>2</c-><c- p>,</c->
<c- f>"columnIndex"</c-><c- p>:</c-> <c- mi>4</c->
<c- p>},</c->
<c- p>{</c->
<c- f>"path"</c-><c- p>:</c-> <c- f>"D/7"</c->
<c- f>"rowIndex"</c-><c- p>:</c-> <c- mi>3</c-><c- p>,</c->
<c- f>"columnIndex"</c-><c- p>:</c-> <c- mi>6</c->
<c- p>}</c->
<c- p>]</c->
<c- p>}</c->
</pre>
<h3 class="heading settled" data-level="3.8" id="well-md"><span class="secno">3.8. </span><span class="content">"well" metadata</span><a class="self-link" href="#well-md"></a></h3>
<p>For high-content screening datasets, the metadata about all fields of views
under a given well can be found under the "well" key in the attributes of the
under a given well can be found under the "well" key in the attributes of the
well group.</p>
<dl>
<dt><strong>images</strong>
<dd>A list of JSON objects defining the fields of views for a given well.
Each object MUST contain a <code>path</code> key identifying the path to the
field of view. If multiple acquisitions were performed in the plate, it
SHOULD contain an <code>acquisition</code> key identifying the id of the
MUST contain an <code>acquisition</code> key identifying the id of the
acquisition which must match one of acquisition JSON objects defined in
the plate metadata.
<dt><strong>version</strong>
<dd>A string defining the version of the specification.
</dl>
<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
view. 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- f>"well"</c-><c- p>:</c-> <c- p>{</c->
<c- f>"images"</c-><c- p>:</c-> <c- p>[</c->
Expand All @@ -2394,6 +2517,23 @@ <h3 class="heading settled" data-level="3.8" id="well-md"><span class="secno">3.
<c- p>],</c->
<c- f>"version"</c-><c- p>:</c-> <c- u>"0.3"</c->
<c- p>}</c->
</pre>
<p>The following JSON object defines a well with two fields of view in a plate with
four acquisitions. The first field is part of the first acquisition, and the second
field is part of the last acquisition.</p>
<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>0</c-><c- p>,</c->
<c- f>"path"</c-><c- p>:</c-> <c- u>"0"</c->
<c- p>},</c->
<c- p>{</c->
<c- f>"acquisition"</c-><c- p>:</c-> <c- mi>3</c-><c- p>,</c->
<c- f>"path"</c-><c- p>:</c-> <c- u>"1"</c->
<c- p>}</c->
<c- p>],</c->
<c- f>"version"</c-><c- p>:</c-> <c- u>"0.1"</c->
<c- p>}</c->
</pre>
<h2 class="heading settled" data-level="4" id="naming-style"><span class="secno">4. </span><span class="content">Specification naming style</span><a class="self-link" href="#naming-style"></a></h2>
<p>Multi-word keys in this specification should use the <code>camelCase</code> style.
Expand Down

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