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Update to MICCAI Tutorial #57

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fedorov Sep 26, 2020
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fedorov Oct 8, 2020
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fedorov Nov 15, 2020
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update to 2021 content
fedorov May 12, 2021
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fedorov Oct 4, 2021
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14 changes: 3 additions & 11 deletions README.md
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# Minimal Theme

[Demo the Theme](http://orderedlist.github.com/minimal/)

This is the raw HTML and styles that are used for the *minimal* theme on [GitHub Pages](http://pages.github.com/).

Syntax highlighting is provided on GitHub Pages by [Pygments](http://pygments.org).

# License

This work is licensed under a [Creative Commons Attribution-ShareAlike 3.0 Unported License](http://creativecommons.org/licenses/by-sa/3.0/).


This is the source for the website located at https://data4miccai.github.io/,
which was put together for the respective tutorial at [MICCAI 2020](https://www.miccai2020.org/en/).

This project is maintained by @fedorov.
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265 changes: 94 additions & 171 deletions index.html
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<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="chrome=1">
<title>Minimal by Steve Smith</title>
<title>DATA4MICCAI: NIH Cancer Imaging Data Repositories for Biomedical Data Science Research</title>

<link rel="stylesheet" href="stylesheets/styles.css">
<link rel="stylesheet" href="stylesheets/pygment_trac.css">
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<body>
<div class="wrapper">
<header>
<h1>Minimal</h1>
<p>A Theme for GitHub Pages</p>
<p class="view"><a href="http://github.com/orderedlist/minimal">View the Project on GitHub <small>orderedlist/minimal</small></a></p>
<ul>
<li><a href="https://github.com/orderedlist/minimal/zipball/master">Download <strong>ZIP File</strong></a></li>
<li><a href="https://github.com/orderedlist/minimal/tarball/master">Download <strong>TAR Ball</strong></a></li>
<li><a href="http://github.com/orderedlist/minimal">Fork On <strong>GitHub</strong></a></li>
</ul>
</header>
<section>
<h1>GitHub Flavored Markdown</h1>

<p><em>View the <a href="http://github.github.com/github-flavored-markdown/sample_content.html">source of this content</a>.</em></p>

<p>Let's get the whole "linebreak" thing out of the way. The next paragraph contains two phrases separated by a single newline character:</p>

<p>Roses are red<br>
Violets are blue</p>
<h1>DATA4MICCAI</h1>

<p>The next paragraph has the same phrases, but now they are separated by two spaces and a newline character:</p>
<h2>A <a href="https://www.miccai2021.org/en/">MICCAI 2021</a> Tutorial</h2>

<p>Roses are red<br><br>
Violets are blue</p>

<p>Oh, and one thing I cannot stand is the mangling of words with multiple underscores in them like perform_complicated_task or do_this_and_do_that_and_another_thing.</p>

<h2>A bit of the GitHub spice</h2>

<p>In addition to the changes in the previous section, certain references are auto-linked:</p>
<a href="https://www.miccai2021.org/en/"><img src="https://www.miccai2021.org/files/images/layout/en/miccai2021-logo.png" alt="MICCAI 2020"></a>
</header>
<section>

<h1>NIH Cancer Imaging Data Repositories for Biomedical Data Science Research</h1>

<h2>Date: Sept 27, 2021</h2>
<h2>Time: 10am-2pm (EDT) / 14:00-18:00 (UTC)</h2>
<br><br>
The National Cancer Institute (NCI), of the National Institutes of Health (NIH), has made significant investments in the
creation and development of public data repositories to enable and promote sharing and secondary analysis of cancer
imaging data through an open science approach. Since its inception in 2011, <a href="https://www.cancerimagingarchive.net/">The Cancer Imaging Archive (TCIA)</a> has
provided the imaging research community with a stable and reliable resource for sharing de-identified clinical
radiology (DICOM), and more recently digital pathology images of a variety of cancers. A growing number of
collections in TCIA contain clinical metadata, annotations, and third-party analysis results.
<br><br>
Recently NCI has launched the <a href="https://datacommons.cancer.gov">Cancer Research Data Commons (CRDC)</a>, an enterprise of cloud-based data
repositories and resources dedicated to key information modalities in cancer research (including genomics,
proteomics, and imaging) to provide the research community with a virtual and expandable infrastructure to enable
cross-domain data analysis and archival. Adhering to FAIR principles in cancer informatics, CRDC aims to further
enable innovations in data science in oncology. <a href="https://imaging.datacommons.cancer.gov">Imaging Data Commons (IDC)</a>,
the imaging node in CRDC, publicly
released in October 2020, connects researchers with image collections from TCIA and beyond, through a robust
infrastructure containing metadata, image-derived data (segmentations, annotations, and image-based analysis
results), allowing image browsing and connectivity to Cloud Resources for image computation, data analysis, and
archival of the results. Direct connectivity of IDC data to robust Google analytics and ML tools is an important feature
of this platform.
<br><br>
This tutorial aims to familiarize attendees with TCIA, IDC, their similarities and differences in features and capabilities,
including search, browsing, downloading (through TCIA), viewing and cohort collection (through IDC), and cloud
computation through the NCI Cloud Resources. All levels are welcome.

Attendees will be able to follow the demonstration session at their own pace, or during the tutorial, following
the learning materials included in the IDC documentation. To be able to follow all of the exercises and demonstration
notebooks the attendees will need to have a Google Cloud Project with billing activated. IDC provides free cloud
credits to facilitate exploration of the resource. The attendees are encouraged to request these credits in advance using
the <a href="https://docs.google.com/forms/d/e/1FAIpQLSfXvXqficGaVEalJI3ym6rKqarmW_YUUWG6A4U8pclvR8MmRQ/viewform">IDC cloud credit application form</a>.
<br><br>

<h2>Agenda</h2>

<b>10:00 – 10:50 am Cancer Imaging Data Repositories</b>
<ul>
<li>SHA: be6a8cc1c1ecfe9489fb51e4869af15a13fc2cd2</li>
<li>User@SHA ref: <a href="https://github.com/mojombo/product/commit/be6a8cc1c1ecfe9489fb51e4869af15a13fc2cd2" class="commit-link">mojombo@<tt>be6a8cc</tt></a></li>
<li>User/Project@SHA: <a href="https://github.com/mojombo/god/commit/be6a8cc1c1ecfe9489fb51e4869af15a13fc2cd2" class="commit-link">mojombo/god@<tt>be6a8cc</tt></a></li>
<li>#Num: <a href="https://github.com/github/product/issues/1" class="issue-link" title="Baseline: What is up in the air right now?">#1</a></li>
<li>User/#Num: mojombo#1</li>
<li>User/Project#Num: <a href="https://github.com/mojombo/god/issues/1" class="issue-link" title="The server is not available (or you do not have permissions to access it)">mojombo/god#1</a></li>
<li>10 am - 10:10 am Introduction – K. Farahani</li> 
<li>10:10 am - 10:30 am The Cancer Imaging Archive (TCIA)– J. Freymann</li>
<li>10:30 am - 10:50 am Imaging Data Commons (IDC) – A. Fedorov, R. Kikinis <a href="https://docs.google.com/presentation/d/17IfcvwCrMkw2On3FZ3EjqjyzI6K_WA5BEXmjzvY9YWY/edit?usp=sharing">(slides)</a></li>
<li>10:50 am – 10:55 am Q &amp; A</li>
<li>10:55 am Break</li>
</ul>

<p>These are dangerous goodies though, and we need to make sure email addresses don't get mangled:</p>

<p>My email addy is <a href="mailto:tom@github.com">tom@github.com</a>.</p>

<h2>Math is hard, let's go shopping</h2>

<p>In first grade I learned that 5 &gt; 3 and 2 &lt; 7. Maybe some arrows. 1 -&gt; 2 -&gt; 3. 9 &lt;- 8 &lt;- 7.</p>

<p>Triangles man! a^2 + b^2 = c^2</p>

<h2>We all like making lists</h2>

<p>The above header should be an H2 tag. Now, for a list of fruits:</p>


<b>11 am – 11:55 am Demonstration session: TCIA Features</b>
<ul>
<li>Red Apples</li>
<li>Purple Grapes</li>
<li>Green Kiwifruits</li>
<li>11:00 am - 11: 15 am Browsing Radiology and Pathology Data – J. Kirby</li> 
<li>11:15 am - 11:30 am Searching with the Radiology Data Portal – L. Tarbox</li>
<li>11:30 am - 11:45 am Additional tools and resources – F. Prior</li>
<li>11:45 am – 11:55 am Q &amp; A</li>
<li>11:55 am Break</li>
</ul>

<b>12 pm – 12:30 pm Project MONAI and public data from TCIA and IDC – S. Aylward</b>
<ul>
<li>12:30 pm – 12:35 pm Q &amp; A</li>
<li>12:35 pm Break</li>
</ul>

<b>12:45 pm – 1:35 pm Demonstration session: IDC Features and Cloud Compute</b>
<ul>
<li>12:45 pm - 1:00 pm Imaging Data Commons Features - A. Fedorov</li> 
<ul>
<li>short demonstration videos available <a href="https://www.youtube.com/playlist?list=PLhawVWNiPvwb2H0D9UTOIL23bc5DuDJRu">here</a></li>
<li>overview paper about IDC published in "Cancer Research" is <a href="http://dx.doi.org/10.1158/0008-5472.CAN-21-0950">here</a></li>
</ul>
<li>1:00 pm - 1:15 pm Introduction to Google Cloud (GCP) Platform – W. Longabaugh <a href="https://docs.google.com/presentation/d/1HNZ34xkZCXt6WRDcEtmAUGNq5TM0xzPaK7sojKJfoBc/edit?usp=sharing">(slides)</a></li> 
<li>1:15 pm - 1:30 pm Utilizing IDC and GCP to support AI imaging research – D. Bontempi</li>
<ul>
<li>IDC notebooks are available <a href="https://github.com/ImagingDataCommons/IDC-Examples/tree/master/notebooks">here</a></li>
</ul>
<li>1:30 pm – 1:45 pm Q &amp;A</li>
</ul>

<p>Let's get crazy:</p>

<ol>
<li>
<p>This is a list item with two paragraphs. Lorem ipsum dolor<br>
sit amet, consectetuer adipiscing elit. Aliquam hendrerit<br>
mi posuere lectus.</p>

<p>Vestibulum enim wisi, viverra nec, fringilla in, laoreet<br>
vitae, risus. Donec sit amet nisl. Aliquam semper ipsum<br>
sit amet velit.</p>
</li>
<li><p>Suspendisse id sem consectetuer libero luctus adipiscing.</p></li>
</ol>

<p>What about some code <strong>in</strong> a list? That's insane, right?</p>

<ol>
<li>
<p>In Ruby you can map like this:</p>

<pre><code>['a', 'b'].map { |x| x.uppercase }</code></pre>
</li>
<li>
<p>In Rails, you can do a shortcut:</p>

<pre><code>['a', 'b'].map(&amp;:uppercase)</code></pre>
</li>
</ol>

<p>Some people seem to like definition lists</p>

<dl>
<dt>Lower cost</dt>
<dd>The new version of this product costs significantly less than the previous one!</dd>
<dt>Easier to use</dt>
<dd>We've changed the product so that it's much easier to use!</dd>
</dl>

<h2>I am a robot</h2>

<p>Maybe you want to print <code>robot</code> to the console 1000 times. Why not?</p>

<pre><code>def robot_invasion
puts("robot " * 1000)
end
</code></pre>

<p>You see, that was formatted as code because it's been indented by four spaces.</p>

<p>How about we throw some angle braces and ampersands in there?</p>

<pre><code>&lt;div class="footer"&gt;
&amp;copy; 2004 Foo Corporation
&lt;/div&gt;
</code></pre>

<h2>Set in stone</h2>

<p>Preformatted blocks are useful for ASCII art:</p>

<pre> ,-.
, ,-. ,-.
/ \ ( )-( )
\ | ,.&gt;-( )-&lt;
\|,' ( )-( )
Y ___`-' `-'
|/__/ `-'
|
|
| -hrr-
___|_____________
</pre>

<h2>Playing the blame game</h2>

<p>If you need to blame someone, the best way to do so is by quoting them:</p>

<blockquote>
<p>I, at any rate, am convinced that He does not throw dice.</p>
</blockquote>

<p>Or perhaps someone a little less eloquent:</p>

<blockquote>
<p>I wish you'd have given me this written question ahead of time so I<br>
could plan for it... I'm sure something will pop into my head here in<br>
the midst of this press conference, with all the pressure of trying to<br>
come up with answer, but it hadn't yet...</p>

<p>I don't want to sound like<br>
I have made no mistakes. I'm confident I have. I just haven't - you<br>
just put me under the spot here, and maybe I'm not as quick on my feet<br>
as I should be in coming up with one.</p>
</blockquote>
<b>1:30 pm – 2:00 pm Open Discussion</b>

<h2>Table for two</h2>
<h3>Organizers</h3>

<table>
<tbody>
<tr>
<th>ID</th>
<th>Name</th>
<th>Rank</th>
</tr>
<tr>
<td>1</td>
<td>Tom Preston-Werner</td>
<td>Awesome</td>
</tr>
<tr>
<td>2</td>
<td>Albert Einstein</td>
<td>Nearly as awesome</td>
</tr>
</tbody>
</table>
<ul>
<li>Keyvan Farahani, National Cancer Institute</li>
<li>Andrey Fedorov, Brigham and Women's Hospital / Harvard Medical School</li>
<li>John Freymann, Fredrick National Laboratory for Cancer Research</li>
<li>Justin Kirby, Fredrick National Laboratory for Cancer Research</li>
<li>Ulrike Wagner, Fredrick National Laboratory for Cancer Research</li>
<li>Fred Prior, University of Arkansas Medical School</li>
<li>Lawrence Tarbox, University of Arkansas Medical School</li>
<li>Bill Longabaugh, Institute for Systems Biology</li>
<li>Suzanne Paquette, Institute for Systems Biology</li>
<li>David Pot, General Dynamics IT</li>
<li>Ron Kikinis, Brigham and Women's Hospital / Harvard Medical School</li>
</ul>

<h2>Crazy linking action</h2>
<a href="https://data4miccai.github.io/index_2020.html">MICCAI 2020 tutorial page</a>

<p>I get 10 times more traffic from <a href="http://google.com/" title="Google">Google</a> than from<br>
<a href="http://search.yahoo.com/" title="Yahoo Search">Yahoo</a> or <a href="http://search.msn.com/" title="MSN Search">MSN</a>.</p>
</section>
<footer>
<p>This project is maintained by <a href="http://github.com/orderedlist">Steve Smith</a></p>
<p>This page is maintained by <a href="http://github.com/fedorov">Andrey Fedorov</a></p>
<p><small>Hosted on GitHub Pages &mdash; Theme by <a href="https://github.com/orderedlist">orderedlist</a></small></p>
</footer>
</div>
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