docs/docs/assays.mibi.mibi_template.html
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<p>
<a href="index.html">CIDC Documentation</a>
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<h1>
MIBI assay template
</h1>
<p>
<b>Description:</b> Multiplexed Ion Beam Imaging (MIBI) submission.
</p>
</div>
<div class="container">
<div class="accordion" id="MIBI_accordion">
<div class="card">
<div class="card-header" id="MIBI">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#MIBI_card" aria-expanded="false" aria-controls="MIBI_card">
Worksheet - MIBI
</button>
</h2>
</div>
<div id="MIBI_card" class="collapse" aria-labelledby="MIBI" data-parent="#MIBI_accordion">
<div class="card-body">
<div class="accordion" id="MIBI_preamble_accordion">
<div class="card">
<div class="card-header" id="MIBI_preamble">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#MIBI_preamble_card" aria-expanded="false" aria-controls="MIBI_preamble_card">
Preamble Rows
</button>
</h2>
</div>
<div id="MIBI_preamble_card" class="collapse" aria-labelledby="MIBI_preamble" data-parent="#MIBI_preamble_accordion">
<div class="card-body">
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="protocol identifier">
protocol identifier
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Trial identifier used by lead organization, ie. Center for Experimental Therapeutics Program (CTEP) ID or Industry Sponsored ID. This is usually a short identifier. Example: E4412.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="batch id">
batch id
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Batch identification number. Unique to every batch.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="assay creator">
assay creator
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Indicates what site is filling out the assay.
</td>
<td>
<
string
>
<ul>
<li>"DFCI"</li>
<li>"Mount Sinai"</li>
<li>"Stanford"</li>
<li>"MD Anderson"</li>
<li>"Adaptive"</li>
<li>"Broad"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="folder">
folder
</span>
</td>
<td width=55%>
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td colspan=3 class="container">
<div class="accordion" id="metadata_tsv_accordion">
<div class="card">
<div class="card-header" id="metadata_tsv">
<div class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#metadata_tsv_card" aria-expanded="false" aria-controls="metadata_tsv_card">
metadata tsv
</button>
<div style="float: right;">
<
>
</div>
</div>
</div>
<div id="metadata_tsv_card" class="collapse" aria-labelledby="metadata_tsv">
<div class="card-body">
Path to file, relative to the intake bucket.
<br>
All files are
<sup><mark>required</mark></sup>
<br>
<table class="table table-striped">
<thead>
<tr>
<th>File name</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
{folder or ""}{metadata_tsv}
</td>
<td width=55%>
Deidentified metadata as a TSV file
</td>
<td>
<a href="files.tsv.html">
tsv
</a>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
<div class="accordion" id="MIBI_body_accordion">
<div class="card">
<div class="card-header" id="MIBI_body">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#MIBI_body_card" aria-expanded="false" aria-controls="MIBI_body_card">
Data Columns
</button>
</h2>
</div>
<div id="MIBI_body_card" class="collapse" aria-labelledby="MIBI_body" data-parent="#MIBI_body_accordion">
<div class="card-body">
<h5 class="text-muted">Samples</h4>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="Cimac id">
Cimac id
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Id of an sample within this clinical trial, that this assay record is based upon.
</td>
<td>
<
string
>
as regex <br> <code>^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$</code>
</td>
</tr>
<tr>
<td>
<span id="Roi id">
Roi id
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Identifier of a region of interest within one mIF slide, e.g. 1, 2, 3 or [123x321]
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="Roi description">
Roi description
</span>
</td>
<td width=55%>
A text description of this ROI. Eg: decidua
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="Comment">
Comment
</span>
</td>
<td width=55%>
A text comment regarding this slide.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td colspan=3 class="container">
<div class="accordion" id="Dataset_accordion">
<div class="card">
<div class="card-header" id="Dataset">
<div class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#Dataset_card" aria-expanded="false" aria-controls="Dataset_card">
Dataset
</button>
<sup><mark>required</mark></sup>
<div style="float: right;">
<
string
>
</div>
</div>
</div>
<div id="Dataset_card" class="collapse" aria-labelledby="Dataset">
<div class="card-body">
<br>
All files are
<sup><mark>required</mark></sup>
<br>
<table class="table table-striped">
<thead>
<tr>
<th>File name</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
{folder or ""}{dataset}/3D_image_stack.ome.tiff
</td>
<td width=55%>
Analysis-ready multichannel image in OME TIFF format
</td>
<td>
<a href="files.image.html">
image
</a>
</td>
</tr>
<tr>
<td>
{folder or ""}{dataset}/Mapping/cluster_labels_image.tif
</td>
<td width=55%>
Cluster-labelled image in TIFF format
</td>
<td>
<a href="files.image.html">
image
</a>
</td>
</tr>
<tr>
<td>
{folder or ""}{dataset}/mcd/channelnames_report.csv
</td>
<td width=55%>
Channel names table in CSV format
</td>
<td>
<a href="files.csv.html">
csv
</a>
</td>
</tr>
<tr>
<td>
{folder or ""}{dataset}/SingleCellData/cells.csv
</td>
<td width=55%>
Single cell data table in CSV format
</td>
<td>
<a href="files.csv.html">
csv
</a>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="accordion" id="Antibodies_accordion">
<div class="card">
<div class="card-header" id="Antibodies">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#Antibodies_card" aria-expanded="false" aria-controls="Antibodies_card">
Worksheet - Antibodies
</button>
</h2>
</div>
<div id="Antibodies_card" class="collapse" aria-labelledby="Antibodies" data-parent="#Antibodies_accordion">
<div class="card-body">
<div class="accordion" id="Antibodies_body_accordion">
<div class="card">
<div class="card-header" id="Antibodies_body">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#Antibodies_body_card" aria-expanded="false" aria-controls="Antibodies_body_card">
Data Columns
</button>
</h2>
</div>
<div id="Antibodies_body_card" class="collapse" aria-labelledby="Antibodies_body" data-parent="#Antibodies_body_accordion">
<div class="card-body">
<h5 class="text-muted">Antibodies</h4>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="Channel id">
Channel id
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
the ID as listed in channel_names files and used in the OME tiffs
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="Antibody name">
Antibody name
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Antibody type collected for this study.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="Scicrunch rrid">
Scicrunch rrid
</span>
</td>
<td width=55%>
the antibody's Research Resource Identifier from SciCrunch
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="Uniprot accession number">
Uniprot accession number
</span>
</td>
<td width=55%>
the UniProt accession number of the target protein
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="Lot number">
Lot number
</span>
</td>
<td width=55%>
Identification number assigned to the particular quantity or lot of material from manufacturer.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="Dilution">
Dilution
</span>
</td>
<td width=55%>
the final working dilution of the stock antibody
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="Concentration value">
Concentration value
</span>
</td>
<td width=55%>
the numeric value of the antibody concentration
</td>
<td>
<
number
>
</td>
</tr>
<tr>
<td>
<span id="Concentration units">
Concentration units
</span>
</td>
<td width=55%>
the units of the concentration value
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="Conjugated catalog number">
Conjugated catalog number
</span>
</td>
<td width=55%>
Antibody registry catalog number assigned to antibody sample.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="Conjugated tag">
Conjugated tag
</span>
</td>
<td width=55%>
the tag to which the antibody is conjugated and used for detection
</td>
<td>
<
string
>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
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