docs/docs/assays.mif.html
<!DOCTYPE html>
<html>
<head>
<title>CIDC Schemas</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous">
<style>
.bd-placeholder-img {
font-size: 1.125rem;
text-anchor: middle;
-webkit-user-select: none;
-moz-user-select: none;
-ms-user-select: none;
user-select: none;
}
@media (min-width: 768px) {
.bd-placeholder-img-lg {
font-size: 3.5rem;
}
}
</style>
</head>
<body>
<main role="main">
<div class="container">
<p>
<a href="index.html">CIDC Documentation</a>
</p>
<h1>
mIF Assay
</h1>
<p>
<b>Description:</b> Multiplex immunofluorescence.
</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="panel">
panel
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
</td>
<td>
<
string
>
<ul>
<li>"Panel 1: PD-L1, CD68, PD-1, CD8, CD3, pan-cytokeratin, DAPI"</li>
<li>"Panel 2: FOXP3, Granzyme B, CD45RO, CD8, CD3, pan-cytokeratin, DAPI"</li>
<li>"Panel 3: pan-cytokeratin, CD8, PD-1, PD-L1, DAPI"</li>
<li>"Panel 4: SOX10, CD8, PD-1, PD-L1, DAPI"</li>
<li>"Not Provided"</li>
</ul>
</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="assay_creator">
assay_creator
</span>
</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="cell_segmentation_model">
cell_segmentation_model
</span>
</td>
<td width=55%>
Model used for cell segmentation in an imaging experiment.
</td>
<td>
<
string
>
<ul>
<li>"proprietary"</li>
<li>"watershed"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="image_analysis_software">
image_analysis_software
</span>
</td>
<td width=55%>
Source software for digital pathology and image analysis.
</td>
<td>
<
string
>
<ul>
<li>"InForm"</li>
<li>"QuPath"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="image_analysis_software_version">
image_analysis_software_version
</span>
</td>
<td width=55%>
Source software version for digital pathology and image analysis.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="imaging_date">
imaging_date
</span>
</td>
<td width=55%>
Date on which imaging experiment was analyzed.
</td>
<td>
<
string
: date
>
</td>
</tr>
<tr>
<td>
<span id="imaging_status">
imaging_status
</span>
</td>
<td width=55%>
Imaging experiment's successful completion.
</td>
<td>
<
string
>
<ul>
<li>"Yes"</li>
<li>"No"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="positive_cell_detection">
positive_cell_detection
</span>
</td>
<td width=55%>
Model used for positive cell detection in imaging experiment.
</td>
<td>
<
string
>
<ul>
<li>"proprietary"</li>
<li>"random forest classifier"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="qc_report">
qc_report
</span>
</td>
<td width=55%>
Information about a ZIP file.
</td>
<td>
<a href="files.zip.html">
zip
</a>
</td>
</tr>
<tr>
<td>
<span id="slide_scanner_model">
slide_scanner_model
</span>
</td>
<td width=55%>
Model version of the slide scanner instrument.
</td>
<td>
<
string
>
<ul>
<li>"Vectra 2.0"</li>
<li>"Hamamatsu"</li>
<li>"VectraPolaris/3.0.3"</li>
<li>"Not Provided"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="staining">
staining
</span>
</td>
<td width=55%>
'manual' or Model version of the autostainer instrument used for tissue sample labeling.
</td>
<td>
<
string
>
<ul>
<li>"manual"</li>
<li>"Bond RX"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="staining_date">
staining_date
</span>
</td>
<td width=55%>
Date on which slide staining was processed.
</td>
<td>
<
string
: date
>
</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>
<sup><mark>required</mark></sup>
<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 on the multiplex immunofluorescence platform.
<br>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="amplification_time">
amplification_time
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Length of time required for amplified signal detection.
</td>
<td>
<
string
: time
>
</td>
</tr>
<tr>
<td>
<span id="antigen_retrieval_time">
antigen_retrieval_time
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Length of time needed for antigen retrieval.
</td>
<td>
<
string
: time
>
</td>
</tr>
<tr>
<td>
<span id="dilutent">
dilutent
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Dilution agent used for antibody sample.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="fluor_dilution">
fluor_dilution
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Concentration ratio for fluor dilution agent.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="fluor_wavelength">
fluor_wavelength
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Wavelength registered for Alexa Fluor processing.
</td>
<td>
<
integer
>
</td>
</tr>
<tr>
<td>
<span id="primary_ab_dilution">
primary_ab_dilution
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Concentration ratio for primary antibody dilution.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="primary_incubation_time">
primary_incubation_time
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Length of time for primary antibody incubation.
</td>
<td>
<
string
: time
>
</td>
</tr>
<tr>
<td>
<span id="antibody">
antibody
</span>
</td>
<td width=55%>
Antibody type collected for this study.
</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="clone">
clone
</span>
</td>
<td width=55%>
Resulting type of antibody clone from primary antibody sample.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="company">
company
</span>
</td>
<td width=55%>
Company from which antibody sample was derived.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="export_name">
export_name
</span>
</td>
<td width=55%>
Name of this antibody in InForm export, e.g. 'CD8 (Opal 520)'
</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="staining_order">
staining_order
</span>
</td>
<td width=55%>
Order of staining applied
</td>
<td>
<
integer
>
</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 mIF 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="files_accordion">
<div class="card">
<div class="card-header" id="files">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#files_card" aria-expanded="false" aria-controls="files_card">
files
</button>
<sup><mark>required</mark></sup>
<div style="float: right;">
<
object
>
</div>
</div>
<div id="files_card" class="collapse" aria-labelledby="files">
<div class="card-body">
mIF assay input files.
<br>
<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="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 [123 x 321]
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="component_data">
component_data
</span>
</td>
<td width=55%>
Information about an image file.
</td>
<td>
<a href="files.image.html">
image
</a>
</td>
</tr>
<tr>
<td>
<span id="composite_image">
composite_image
</span>
</td>
<td width=55%>
Information about an image file.
</td>
<td>
<a href="files.image.html">
image
</a>
</td>
</tr>
<tr>
<td>
<span id="im3">
im3
</span>
</td>
<td width=55%>
Information about an image file.
</td>
<td>
<a href="files.image.html">
image
</a>
</td>
</tr>
<tr>
<td colspan=3 class="container">
<div class="accordion" id="exports_accordion">
<div class="card">
<div class="card-header" id="exports">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#exports_card" aria-expanded="false" aria-controls="exports_card">
exports
</button>
<sup><mark>required</mark></sup>
<div style="float: right;">
<
array
>
</div>
</div>
<div id="exports_card" class="collapse" aria-labelledby="exports">
<div class="card-body">
An analysis export from inForm of a region of interest (ROI).
<br>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="cell_seg_data">
cell_seg_data
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Data produced from the analysis of cellular image.
</td>
<td>
<a href="files.text.html">
text
</a>
</td>
</tr>
<tr>
<td>
<span id="cell_seg_data_summary">
cell_seg_data_summary
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Summary of the results of a cell segmentation data experiment.
</td>
<td>
<a href="files.text.html">
text
</a>
</td>
</tr>
<tr>
<td>
<span id="export_id">
export_id
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Name used for an inForm export of a region of interest within one mIF slide, e.g. CD8, CD45RO
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="binary_seg_maps">
binary_seg_maps
</span>
</td>
<td width=55%>
Results of a computer vision task, in which specific regions of a region are mapped with binary values.
</td>
<td>
<a href="files.image.html">
image
</a>
</td>
</tr>
<tr>
<td>
<span id="image_with_all_seg">
image_with_all_seg
</span>
</td>
<td width=55%>
Results of a computer vision task, in which specific regions of a region are mapped.
</td>
<td>
<a href="files.image.html">
image
</a>
</td>
</tr>
<tr>
<td>
<span id="image_with_cell_seg_map">
image_with_cell_seg_map
</span>
</td>
<td width=55%>
Results of a computer vision task, in which specific regions of a region are mapped.
</td>
<td>
<a href="files.image.html">
image
</a>
</td>
</tr>
<tr>
<td>
<span id="image_with_phenotype_map">
image_with_phenotype_map
</span>
</td>
<td width=55%>
Image produced from the combination of multiple imaging experiment data images.
</td>
<td>
<a href="files.image.html">
image
</a>
</td>
</tr>
<tr>
<td>
<span id="image_with_tissue_seg">
image_with_tissue_seg
</span>
</td>
<td width=55%>
Results of a computer vision task, in which specific regions of a region are mapped.
</td>
<td>
<a href="files.image.html">
image
</a>
</td>
</tr>
<tr>
<td>
<span id="phenotype_map">
phenotype_map
</span>
</td>
<td width=55%>
Image produced from the combination of multiple imaging experiment data images.
</td>
<td>
<a href="files.image.html">
image
</a>
</td>
</tr>
<tr>
<td>
<span id="score_data">
score_data
</span>
</td>
<td width=55%>
Generation of values based on experiment data.
</td>
<td>
<a href="files.text.html">
text
</a>
</td>
</tr>
<tr>
<td>
<span id="tissue_seg_data">
tissue_seg_data
</span>
</td>
<td width=55%>
Data produced from the analysis of tissue image.
</td>
<td>
<a href="files.text.html">
text
</a>
</td>
</tr>
<tr>
<td>
<span id="tissue_seg_data_summary">
tissue_seg_data_summary
</span>
</td>
<td width=55%>
Summary of the results of a tissue segmentation data experiment.
</td>
<td>
<a href="files.text.html">
text
</a>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</td>
</tr>
<tr>
<td colspan=3 class="container">
<div class="accordion" id="excluded_samples_accordion">
<div class="card">
<div class="card-header" id="excluded_samples">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#excluded_samples_card" aria-expanded="false" aria-controls="excluded_samples_card">
excluded_samples
</button>
<div style="float: right;">
<
array
>
</div>
</div>
<div id="excluded_samples_card" class="collapse" aria-labelledby="excluded_samples">
<div class="card-body">
A list of samples excluded from analysis, along with the reasons why.
<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%>
Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as CTTTPPPSS.AA for trial code TTT, participant PPP, sample SS, and aliquot AA.
</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="reason_excluded">
reason_excluded
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
A comment describing why this sample is missing from the pipeline output.
</td>
<td>
<
string
>
</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.mif.mif_template.html'>
mIF assay template
</a>
</td>
<td>
Multiplex ImmunoFlouresence (mIF) submission.
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</div>
</main>
<script src="https://code.jquery.com/jquery-3.3.1.slim.min.js" integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.7/umd/popper.min.js" integrity="sha384-UO2eT0CpHqdSJQ6hJty5KVphtPhzWj9WO1clHTMGa3JDZwrnQq4sF86dIHNDz0W1" crossorigin="anonymous"></script>
<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/js/bootstrap.min.js" integrity="sha384-JjSmVgyd0p3pXB1rRibZUAYoIIy6OrQ6VrjIEaFf/nJGzIxFDsf4x0xIM+B07jRM" crossorigin="anonymous"></script>
</body>
</html>