docs/docs/assays.mif.mif_template.html
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<p>
<a href="index.html">CIDC Documentation</a>
</p>
<h1>
mIF assay template
</h1>
<p>
<b>Description:</b> Multiplex ImmunoFlouresence (mIF) submission.
</p>
</div>
<div class="container">
<div class="accordion" id="mIF_accordion">
<div class="card">
<div class="card-header" id="mIF">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#mIF_card" aria-expanded="false" aria-controls="mIF_card">
Worksheet - mIF
</button>
</h2>
</div>
<div id="mIF_card" class="collapse" aria-labelledby="mIF" data-parent="#mIF_accordion">
<div class="card-body">
<div class="accordion" id="mIF_preamble_accordion">
<div class="card">
<div class="card-header" id="mIF_preamble">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#mIF_preamble_card" aria-expanded="false" aria-controls="mIF_preamble_card">
Preamble Rows
</button>
</h2>
</div>
<div id="mIF_preamble_card" class="collapse" aria-labelledby="mIF_preamble" data-parent="#mIF_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="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="slide scanner model">
slide scanner model
</span>
<br><sup><mark>required</mark></sup>
</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="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="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="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="positive cell detection model">
positive cell detection model
</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="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>
<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="report">
report
</span>
</td>
<td width=55%>
Information about a ZIP file.
</td>
<td>
<a href="files.zip.html">
zip
</a>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
<div class="accordion" id="mIF_body_accordion">
<div class="card">
<div class="card-header" id="mIF_body">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#mIF_body_card" aria-expanded="false" aria-controls="mIF_body_card">
Data Columns
</button>
</h2>
</div>
<div id="mIF_body_card" class="collapse" aria-labelledby="mIF_body" data-parent="#mIF_body_accordion">
<div class="card-body">
<h5 class="text-muted">ROIs</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 [123 x 321]
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="IM3 file">
IM3 file
</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="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>
</table>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="accordion" id="Exports_accordion">
<div class="card">
<div class="card-header" id="Exports">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#Exports_card" aria-expanded="false" aria-controls="Exports_card">
Worksheet - Exports
</button>
</h2>
</div>
<div id="Exports_card" class="collapse" aria-labelledby="Exports" data-parent="#Exports_accordion">
<div class="card-body">
<div class="accordion" id="Exports_preamble_accordion">
<div class="card">
<div class="card-header" id="Exports_preamble">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#Exports_preamble_card" aria-expanded="false" aria-controls="Exports_preamble_card">
Preamble Rows
</button>
</h2>
</div>
<div id="Exports_preamble_card" class="collapse" aria-labelledby="Exports_preamble" data-parent="#Exports_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>
</table>
</div>
</div>
</div>
</div>
<div class="accordion" id="Exports_body_accordion">
<div class="card">
<div class="card-header" id="Exports_body">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#Exports_body_card" aria-expanded="false" aria-controls="Exports_body_card">
Data Columns
</button>
</h2>
</div>
<div id="Exports_body_card" class="collapse" aria-labelledby="Exports_body" data-parent="#Exports_body_accordion">
<div class="card-body">
<h5 class="text-muted">Exports</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 [123 x 321]
</td>
<td>
<
string
>
</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="Score data files">
Score data files
</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 colspan=3 class="container">
<div class="accordion" id="inForm_export_prefix_accordion">
<div class="card">
<div class="card-header" id="inForm_export_prefix">
<div class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#inForm_export_prefix_card" aria-expanded="false" aria-controls="inForm_export_prefix_card">
inForm export prefix
</button>
<sup><mark>required</mark></sup>
<div style="float: right;">
<
string
>
</div>
</div>
</div>
<div id="inForm_export_prefix_card" class="collapse" aria-labelledby="inForm_export_prefix">
<div class="card-body">
Path on a user's computer to an InForm export directory with ROI's export prefix. From that upload tool will look for binary_seg_maps.tif, cell_seg_data.txt, cell_seg_data_summary.txt, phenotype_map.tif, composite_image.tif, and component_data.tif
<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>
binary_seg_maps.tif
</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>
cell_seg_data.txt
</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>
cell_seg_data_summary.txt
</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>
phenotype_map.tif
</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>
tissue_seg_data.txt
</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>
tissue_seg_data_summary.txt
</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>
<tr>
<td>
image_with_all_seg.tif
</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>
image_with_cell_seg_map.tif
</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>
image_with_phenotype_map.tif
</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>
image_with_tissue_seg.tif
</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>
</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="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="Export name">
Export name
</span>
<br><sup><mark>required</mark></sup>
</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="Clone">
Clone
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Resulting type of antibody clone from primary antibody sample.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="Antibody Company">
Antibody Company
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Company from which antibody sample was derived.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="Cat#">
Cat#
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Antibody registry catalog number assigned to antibody sample.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="Lot#">
Lot#
</span>
<br><sup><mark>required</mark></sup>
</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>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Order of staining applied
</td>
<td>
<
integer
>
</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="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="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="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="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>
</table>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="accordion" id="Excluded_Samples_accordion">
<div class="card">
<div class="card-header" id="Excluded_Samples">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#Excluded_Samples_card" aria-expanded="false" aria-controls="Excluded_Samples_card">
Worksheet - Excluded Samples
</button>
</h2>
</div>
<div id="Excluded_Samples_card" class="collapse" aria-labelledby="Excluded_Samples" data-parent="#Excluded_Samples_accordion">
<div class="card-body">
<div class="accordion" id="Excluded_Samples_body_accordion">
<div class="card">
<div class="card-header" id="Excluded_Samples_body">
<h2 class="mb-0">
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Data Columns
</button>
</h2>
</div>
<div id="Excluded_Samples_body_card" class="collapse" aria-labelledby="Excluded_Samples_body" data-parent="#Excluded_Samples_body_accordion">
<div class="card-body">
<h5 class="text-muted">Samples Excluded From Analysis</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%>
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">
reason
</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>
</div>
</div>
</div>
</div>
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