diff --git a/README.md b/README.md index cf323a5be..06fdddce4 100644 --- a/README.md +++ b/README.md @@ -1,14 +1,6 @@ # 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. diff --git a/assets/miccai-2020-logo.png b/assets/miccai-2020-logo.png new file mode 100644 index 000000000..0b7f33db3 Binary files /dev/null and b/assets/miccai-2020-logo.png differ diff --git a/index.html b/index.html index 18c29f0bd..b4d55b52c 100644 --- a/index.html +++ b/index.html @@ -3,7 +3,7 @@ - Minimal by Steve Smith + DATA4MICCAI: NIH Cancer Imaging Data Repositories for Biomedical Data Science Research @@ -15,190 +15,113 @@
-

Minimal

-

A Theme for GitHub Pages

-

View the Project on GitHub orderedlist/minimal

- -
-
-

GitHub Flavored Markdown

- -

View the source of this content.

- -

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

- -

Roses are red
- Violets are blue

+

DATA4MICCAI

-

The next paragraph has the same phrases, but now they are separated by two spaces and a newline character:

+

A MICCAI 2021 Tutorial

-

Roses are red

- Violets are blue

- -

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.

- -

A bit of the GitHub spice

- -

In addition to the changes in the previous section, certain references are auto-linked:

+ MICCAI 2020 + +
+

NIH Cancer Imaging Data Repositories for Biomedical Data Science Research

+ +

Date: Sept 27, 2021

+

Time: 10am-2pm (EDT) / 14:00-18:00 (UTC)

+

+ 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, The Cancer Imaging Archive (TCIA) 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. +

+Recently NCI has launched the Cancer Research Data Commons (CRDC), 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. Imaging Data Commons (IDC), +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. +

+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 IDC cloud credit application form. +

+ +

Agenda

+ + 10:00 – 10:50 am Cancer Imaging Data Repositories
    -
  • SHA: be6a8cc1c1ecfe9489fb51e4869af15a13fc2cd2
    • -
  • User@SHA ref: mojombo@be6a8cc
    • -
  • User/Project@SHA: mojombo/god@be6a8cc
    • -
  • #Num: #1
    • -
  • User/#Num: mojombo#1
    • -
  • User/Project#Num: mojombo/god#1
    • +
  • 10 am - 10:10 am Introduction – K. Farahani
    •   +
  • 10:10 am - 10:30 am The Cancer Imaging Archive (TCIA)– J. Freymann
    • +
  • 10:30 am - 10:50 am Imaging Data Commons (IDC) – A. Fedorov, R. Kikinis (slides)
    • +
  • 10:50 am – 10:55 am Q & A
    • +
  • 10:55 am Break
- -

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

- -

My email addy is tom@github.com.

- -

Math is hard, let's go shopping

- -

In first grade I learned that 5 > 3 and 2 < 7. Maybe some arrows. 1 -> 2 -> 3. 9 <- 8 <- 7.

- -

Triangles man! a^2 + b^2 = c^2

- -

We all like making lists

- -

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

- + + 11 am – 11:55 am Demonstration session: TCIA Features
    -
  • Red Apples
    • -
  • Purple Grapes
    • -
  • Green Kiwifruits
    • +
  • 11:00 am - 11: 15 am Browsing Radiology and Pathology Data – J. Kirby
    •   +
  • 11:15 am - 11:30 am Searching with the Radiology Data Portal – L. Tarbox
    • +
  • 11:30 am - 11:45 am Additional tools and resources – F. Prior
    • +
  • 11:45 am – 11:55 am Q & A
    • +
  • 11:55 am Break
    • +
+ + 12 pm – 12:30 pm Project MONAI and public data from TCIA and IDC – S. Aylward +
    +
  • 12:30 pm – 12:35 pm Q & A
    • +
  • 12:35 pm Break
    • +
+ + 12:45 pm – 1:35 pm Demonstration session: IDC Features and Cloud Compute +
    +
  • 12:45 pm - 1:00 pm Imaging Data Commons Features - A. Fedorov
    •   +
      +
    • short demonstration videos available here
      • +
    • overview paper about IDC published in "Cancer Research" is here
      • +
    +
  • 1:00 pm - 1:15 pm Introduction to Google Cloud (GCP) Platform – W. Longabaugh (slides)
    •   +
  • 1:15 pm - 1:30 pm Utilizing IDC and GCP to support AI imaging research – D. Bontempi
    • +
      +
    • IDC notebooks are available here
      • +
    +
  • 1:30 pm – 1:45 pm Q &A
-

Let's get crazy:

- -
    -
  1. -

    This is a list item with two paragraphs. Lorem ipsum dolor
    - sit amet, consectetuer adipiscing elit. Aliquam hendrerit
    - mi posuere lectus.

    - -

    Vestibulum enim wisi, viverra nec, fringilla in, laoreet
    - vitae, risus. Donec sit amet nisl. Aliquam semper ipsum
    - sit amet velit.

    -
    2. -

  2. Suspendisse id sem consectetuer libero luctus adipiscing.

    3. -
- -

What about some code in a list? That's insane, right?

- -
    -
  1. -

    In Ruby you can map like this:

    - - 
    ['a', 'b'].map { |x| x.uppercase }
    -
    2. -
  2. -

    In Rails, you can do a shortcut:

    - - 
    ['a', 'b'].map(&:uppercase)
    -
    3. -
- -

Some people seem to like definition lists

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

I am a robot

- -

Maybe you want to print robot to the console 1000 times. Why not?

- - 
def robot_invasion
-  puts("robot " * 1000)
-end
-
- -

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

- -

How about we throw some angle braces and ampersands in there?

- - 
<div class="footer">
-    &copy; 2004 Foo Corporation
-</div>
-
- -

Set in stone

- -

Preformatted blocks are useful for ASCII art:

- - 
             ,-.
-    ,     ,-.   ,-.
-   / \   (   )-(   )
-   \ |  ,.>-(   )-<
-    \|,' (   )-(   )
-     Y ___`-'   `-'
-     |/__/   `-'
-     |
-     |
-     |    -hrr-
-  ___|_____________
-
- -

Playing the blame game

- -

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

- -
-

I, at any rate, am convinced that He does not throw dice.

-
- -

Or perhaps someone a little less eloquent:

- -
-

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

- -

I don't want to sound like
- I have made no mistakes. I'm confident I have. I just haven't - you
- just put me under the spot here, and maybe I'm not as quick on my feet
- as I should be in coming up with one.

-
+ 1:30 pm – 2:00 pm Open Discussion -

Table for two

+

Organizers

- - - - - - - - - - - - - - - - - - -
IDNameRank
1Tom Preston-WernerAwesome
2Albert EinsteinNearly as awesome
+
    +
  • Keyvan Farahani, National Cancer Institute
    • +
  • Andrey Fedorov, Brigham and Women's Hospital / Harvard Medical School
    • +
  • John Freymann, Fredrick National Laboratory for Cancer Research
    • +
  • Justin Kirby, Fredrick National Laboratory for Cancer Research
    • +
  • Ulrike Wagner, Fredrick National Laboratory for Cancer Research
    • +
  • Fred Prior, University of Arkansas Medical School
    • +
  • Lawrence Tarbox, University of Arkansas Medical School
    • +
  • Bill Longabaugh, Institute for Systems Biology
    • +
  • Suzanne Paquette, Institute for Systems Biology
    • +
  • David Pot, General Dynamics IT
    • +
  • Ron Kikinis, Brigham and Women's Hospital / Harvard Medical School
    • +
-

Crazy linking action

+ MICCAI 2020 tutorial page -

I get 10 times more traffic from Google than from
- Yahoo or MSN.

diff --git a/index_2020.html b/index_2020.html new file mode 100644 index 000000000..e83896cef --- /dev/null +++ b/index_2020.html @@ -0,0 +1,97 @@ + + + + + + DATA4MICCAI: Public Cancer Imaging Data Repositories for Biomedical Data Science Research + + + + + + + +
+
+

DATA4MICCAI

+ +

A MICCAI 2020 Tutorial

+ + MICCAI 2020 +
+
+ +

Public Cancer Imaging Data Repositories for Biomedical Data Science Research

+ +

Date: Oct 8

+

Time: 10 am EST (2 pm UTC)

+ + The National Cancer Institute (NCI), of the National Institutes of Health (NIH), has made significant investments in 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, The Cancer Imaging Archive (TCIA) 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. +

+ Recently NCI has launched the Cancer Research Data Commons (CRDC), 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. Imaging Data Commons (IDC), the imaging node in CRDC, due for public release in October 2020, will connect 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. +

+ This tutorial aims to familiarize the 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. +

+ The learning objectives of this tutorial include: +
+
    +
  1. To learn about the NCI public image repositories, their similarities and differences.
    2. +
  2. To learn about the capabilities and features offered by each repository.
    3. +
  3. To be able to search for and identify imaging collections of interest and prepare them for further analysis.
    4. +
+ +

Agenda

+ +

Overall introduction - Keyvan Farahani | 5 min

+ +

Session 1: The Cancer Imaging Archive (TCIA) | 50 min

+ + + +

Coffee break | 15 min

+ +

Session 2: Imaging Data Commons (IDC) | 50 min

+ + + +

Summary and wrap-up - Keyvan Farahani | 10 min

+ +

Organizers

+ + + +
+ +
+ + +