docs/docs/assays.mibi.html
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<p>
<a href="index.html">CIDC Documentation</a>
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<h1>
MIBI Assay
</h1>
<p>
<b>Description:</b> Multiplexed Ion Beam Imaging (MIBI) assay
</p>
</div>
<div class="container">
<div class="accordion" id="assay_accordion">
<div class="card">
<div class="card-header" id="assay_metadata">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#assay_metadata_card" aria-expanded="false" aria-controls="assay_metadata_card">
Assay Metadata
</button>
</h2>
</div>
<div id="assay_metadata_card" class="collapse" aria-labelledby="assay_metadata" data-parent="#assay_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="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="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="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="metadata_tsv">
metadata_tsv
</span>
</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 class="card">
<div class="card-header" id="assay_data">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#assay_data_card" aria-expanded="false" aria-controls="assay_data_card">
Assay Data
</button>
</h2>
</div>
<div id="assay_data_card" class="collapse" aria-labelledby="assay_data" data-parent="#assay_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 colspan=3 class="container">
<div class="accordion" id="antibodies_accordion">
<div class="card">
<div class="card-header" id="antibodies">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#antibodies_card" aria-expanded="false" aria-controls="antibodies_card">
antibodies
</button>
<div style="float: right;">
<
array
>
</div>
</div>
<div id="antibodies_card" class="collapse" aria-labelledby="antibodies">
<div class="card-body">
Data specific to antibody preparation for the MIBI assay.
<br>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="antibody">
antibody
</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="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="cat_num">
cat_num
</span>
</td>
<td width=55%>
Antibody registry catalog number assigned to antibody sample.
</td>
<td>
<
string
>
</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="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="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>
<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="lot_num">
lot_num
</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="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>
</table>
</div>
</div>
</div>
</div>
</td>
</tr>
<tr>
<td colspan=3 class="container">
<div class="accordion" id="records_accordion">
<div class="card">
<div class="card-header" id="records">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#records_card" aria-expanded="false" aria-controls="records_card">
records
</button>
<sup><mark>required</mark></sup>
<div style="float: right;">
<
array
>
</div>
</div>
<div id="records_card" class="collapse" aria-labelledby="records">
<div class="card-body">
A single data record from a MIBI assay.
<br>
<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 colspan=3 class="container">
<div class="accordion" id="regions_of_interest_accordion">
<div class="card">
<div class="card-header" id="regions_of_interest">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#regions_of_interest_card" aria-expanded="false" aria-controls="regions_of_interest_card">
regions_of_interest
</button>
<sup><mark>required</mark></sup>
<div style="float: right;">
<
array
>
</div>
</div>
<div id="regions_of_interest_card" class="collapse" aria-labelledby="regions_of_interest">
<div class="card-body">
A region of interest (ROI) is a portion of an image which has been analyzed using image processing software.
<br>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<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="channel_names">
channel_names
</span>
</td>
<td width=55%>
Channel names table in CSV format
</td>
<td>
<a href="files.csv.html">
csv
</a>
</td>
</tr>
<tr>
<td>
<span id="cluster_labels">
cluster_labels
</span>
</td>
<td width=55%>
Cluster-labelled image in TIFF format
</td>
<td>
<a href="files.image.html">
image
</a>
</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>
<span id="multichannel_image">
multichannel_image
</span>
</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>
<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="single_cell_table">
single_cell_table
</span>
</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>
</td>
</tr>
</table>
</div>
</div>
</div>
<div class="card">
<div class="card-header" id="assay_uploads">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#assay_uploads_card" aria-expanded="false" aria-controls="assay_uploads_card">
Assay Uploads
</button>
</h2>
</div>
<div id="assay_uploads_card" class="collapse" aria-labelledby="assay_uploads" data-parent="#assay_accordion">
<div class="card-body">
<table class="table table-striped">
<thead>
<tr>
<th>Entity</th>
<th>Description</th>
</tr>
</thead>
<tr>
<td width=25%>
<a href='assays.mibi.mibi_template.html'>
MIBI assay template
</a>
</td>
<td>
Multiplexed Ion Beam Imaging (MIBI) submission.
</td>
</tr>
</table>
</div>
</div>
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