From 4df536eea56d1cfe1b89657ee43c8c4c407e8bf5 Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Fri, 14 Aug 2020 16:26:51 -0400 Subject: [PATCH 01/50] populate initial content --- index.html | 194 ++++++++--------------------------------------------- 1 file changed, 28 insertions(+), 166 deletions(-) diff --git a/index.html b/index.html index 18c29f0bd..6b214792f 100644 --- a/index.html +++ b/index.html @@ -3,7 +3,7 @@ - Minimal by Steve Smith + Public Cancer Imaging Data Repositories for Biomedical Data Science Research and Education @@ -15,190 +15,52 @@
-

Minimal

-

A Theme for GitHub Pages

-

View the Project on GitHub orderedlist/minimal

- +

DATA4MICCAI

+

A MICCAI 2020 Tutorial

-

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

+

Tutorial outline

-

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

+

Discuss overall goals here

-

Roses are red

- Violets are blue

+

Discuss TCIA here

-

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.

+

Discuss IDC here

-

A bit of the GitHub spice

+

Preliminary agenda

-

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

+

Session 1: TCIA

    -
  • 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
    • +
  • introduction | 10 min
    • +
  • TCIA presentation | 20 min
    • +
  • TCIA hands-on demo | 45 min
-

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:

+

Session 2: IDC

    -
  • Red Apples
    • -
  • Purple Grapes
    • -
  • Green Kiwifruits
    • +
  • introduction | 10 min
    • +
  • IDC presentation | 20 min
    • +
  • IDC hands-on demo | 45 min
-

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.

-
- -

Table for two

- - - - - - - - - - - - - - - - - - - -
IDNameRank
1Tom Preston-WernerAwesome
2Albert EinsteinNearly as awesome
+

Organizers

-

Crazy linking action

+
    +
  • Keyvan Farahani
    • +
  • Andrey Fedorov
    • +
  • John Freymann
    • +
  • Justin Kirby
    • +
  • Todd Pihl
    • +
  • Fred Prior (?)
    • +
  • Ron Kikinis (?)
    • +
  • Others (?)
    • +
-

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

From c4935ab2a13fbbcf8e14f5d6bc3f67a297d0a0da Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Fri, 14 Aug 2020 16:29:46 -0400 Subject: [PATCH 02/50] updates --- index.html | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/index.html b/index.html index 6b214792f..3f71b1e94 100644 --- a/index.html +++ b/index.html @@ -3,7 +3,7 @@ - Public Cancer Imaging Data Repositories for Biomedical Data Science Research and Education + DICOM4MICCAI: Public Cancer Imaging Data Repositories for Biomedical Data Science Research and Education @@ -16,6 +16,7 @@

DATA4MICCAI

+

Public Cancer Imaging Data Repositories for Biomedical Data Science Research and Education

A MICCAI 2020 Tutorial

From 06581b3388d2919f15fd17e99bb98f81635f6bab Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Fri, 14 Aug 2020 16:31:17 -0400 Subject: [PATCH 03/50] updates --- index.html | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/index.html b/index.html index 3f71b1e94..ac6208b53 100644 --- a/index.html +++ b/index.html @@ -16,11 +16,14 @@

DATA4MICCAI

-

Public Cancer Imaging Data Repositories for Biomedical Data Science Research and Education

+

A MICCAI 2020 Tutorial

-

Tutorial outline

+ +

Public Cancer Imaging Data Repositories for Biomedical Data Science Research and Education

+ +

Tutorial outline

Discuss overall goals here

@@ -28,9 +31,9 @@

Tutorial outline

Discuss IDC here

-

Preliminary agenda

+

Preliminary agenda

-

Session 1: TCIA

+

Session 1: TCIA

  • introduction | 10 min
    • @@ -38,7 +41,7 @@

    Session 1: TCIA

  • TCIA hands-on demo | 45 min
-

Session 2: IDC

+

Session 2: IDC

  • introduction | 10 min
    • @@ -46,7 +49,7 @@

    Session 2: IDC

  • IDC hands-on demo | 45 min
-

Organizers

+

Organizers

  • Keyvan Farahani
    • From 9ea3d548de33d37a1eb8d97c4e03c46be5c7e61c Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Sat, 15 Aug 2020 15:30:42 -0400 Subject: [PATCH 04/50] add more content --- index.html | 35 ++++++++++++++++++++++++++++------- 1 file changed, 28 insertions(+), 7 deletions(-) diff --git a/index.html b/index.html index ac6208b53..e6f0a8060 100644 --- a/index.html +++ b/index.html @@ -21,15 +21,36 @@

    DATA4MICCAI

    -

    Public Cancer Imaging Data Repositories for Biomedical Data Science Research and Education

    +

    Public Cancer Imaging Data Repositories for Biomedical Data Science Research and Education

    -

    Tutorial outline

    + The National Cancer Institute (NCI) 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. The 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: -

    Discuss overall goals here

    - -

    Discuss TCIA here

    - -

    Discuss IDC here

    +
      +
    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. +

    Preliminary agenda

    From be1c46428f01051aa75bc3664f7d1dda3ea5000a Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Sat, 15 Aug 2020 15:34:15 -0400 Subject: [PATCH 05/50] updates --- index.html | 29 +++++++---------------------- 1 file changed, 7 insertions(+), 22 deletions(-) diff --git a/index.html b/index.html index e6f0a8060..ec6b162b9 100644 --- a/index.html +++ b/index.html @@ -23,29 +23,14 @@

    DATA4MICCAI

    Public Cancer Imaging Data Repositories for Biomedical Data Science Research and Education

    - The National Cancer Institute (NCI) 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. The 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 National Cancer Institute (NCI) 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. The 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. To learn about the capabilities and features offered by each repository.
      3. From 1443c05e7520993d893092d2d0c1e3fcec6d73c3 Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Sat, 15 Aug 2020 15:34:52 -0400 Subject: [PATCH 06/50] updates --- index.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index.html b/index.html index ec6b162b9..9d4c19aa8 100644 --- a/index.html +++ b/index.html @@ -70,7 +70,7 @@

      Organizers

From 790fa7e4625f1df31b437c45cc613ac6841e6715 Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Sat, 15 Aug 2020 15:35:30 -0400 Subject: [PATCH 07/50] update --- index.html | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/index.html b/index.html index 9d4c19aa8..501aed3ec 100644 --- a/index.html +++ b/index.html @@ -24,11 +24,11 @@

DATA4MICCAI

Public Cancer Imaging Data Repositories for Biomedical Data Science Research and Education

The National Cancer Institute (NCI) 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. The 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:
    From f1300f06b52a2c2d7fc3647f76669df572aee62e Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Sat, 15 Aug 2020 15:36:14 -0400 Subject: [PATCH 08/50] updates --- index.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index.html b/index.html index 501aed3ec..7f1640651 100644 --- a/index.html +++ b/index.html @@ -17,7 +17,7 @@

    DATA4MICCAI

    -

    A MICCAI 2020 Tutorial

    +

    A MICCAI 2020 Tutorial

    From d9c558970a3079bcd8747d5dc02f2c964cbe1e86 Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Mon, 17 Aug 2020 10:43:24 -0400 Subject: [PATCH 09/50] update --- index.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index.html b/index.html index 7f1640651..a54f09afe 100644 --- a/index.html +++ b/index.html @@ -3,7 +3,7 @@ - DICOM4MICCAI: Public Cancer Imaging Data Repositories for Biomedical Data Science Research and Education + DICOM4MICCAI: Public Cancer Imaging Data Repositories for Biomedical Data Science Research From ce68f3bf42fd8c8c91b7c0e62e094fc0795e59d1 Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Mon, 17 Aug 2020 13:18:08 -0400 Subject: [PATCH 10/50] update --- index.html | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/index.html b/index.html index a54f09afe..0b2faa250 100644 --- a/index.html +++ b/index.html @@ -23,9 +23,9 @@

    A MICCAI 2020 Tutorial

    Public Cancer Imaging Data Repositories for Biomedical Data Science Research and Education

    - The National Cancer Institute (NCI) 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. + 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. The 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. + 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.

    From c730cd5d7fc544f479ba18ad47e2f0dbed6633e9 Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Mon, 17 Aug 2020 14:33:44 -0400 Subject: [PATCH 11/50] updates --- index.html | 3 --- 1 file changed, 3 deletions(-) diff --git a/index.html b/index.html index 0b2faa250..1ec6e6bee 100644 --- a/index.html +++ b/index.html @@ -63,9 +63,6 @@

    Organizers

  1. John Freymann
  2. Justin Kirby
  3. Todd Pihl
    4. -
  4. Fred Prior (?)
    5. -
  5. Ron Kikinis (?)
    6. -
  6. Others (?)
    7. 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zQaWXoHY}1=^!ix!g55Ud(H>tXaj8>aw?J}AS;9y$8rz|ee$66Wgp@gy*|-v%9i#{B zxQl@K5rE6W?!5h+Djn(n0mg3N%|3F2UbWHsh8QWZ| zI3gZvxt7as0qB2)e|#|i*+-^{J#`T>t<~N&pb?bDbf&?g^7aBklDf7C3St)Y7InG~ z<73%Rny4x)*WKObx2G$uDleq{R!6DM3NdvG126Kcu^fg?V#QWT0Z-GxlE=;muZPyT za*N5#Byi&p1c)}+7kQ7c_&A0RbH!?Cs4ZnvJcK%jbxPmggRK770CGMnRHP=DeSsY)-5x#u{j7m@+v8kP5QtQZrJWdN~<7sA43P8F=+b!jEKfi?|g2I>sT^drjkcX z+(|BGnvR66DV~^*2MPJ__?Grf7izM3_d)UT?>hVsT^rcV7OElrBoit7Ru@|Xbv#Zh zJK?%bh7KJ9)P@vndL??01woD=b_{LeKN$eR2K>Vq|9$)aeUzr_dxa-}ddSG(%+1-m Qg@SzKq?9FV#Z5#154Ma}n*aa+ literal 0 HcmV?d00001 diff --git a/index.html b/index.html index 1ec6e6bee..0ef30c1a7 100644 --- a/index.html +++ b/index.html @@ -18,6 +18,8 @@

    DATA4MICCAI

    A MICCAI 2020 Tutorial

    + + Italian Trulli
    From b0a708fa488b2c353961a6ce671376c6ab16c776 Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Tue, 18 Aug 2020 10:54:43 -0400 Subject: [PATCH 13/50] add affiliations --- index.html | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/index.html b/index.html index 0ef30c1a7..8132bc88d 100644 --- a/index.html +++ b/index.html @@ -60,11 +60,11 @@

    Session 2: IDC

    Organizers

      -
    • Keyvan Farahani
      • -
    • Andrey Fedorov
      • -
    • John Freymann
      • -
    • Justin Kirby
      • -
    • Todd Pihl
      • +
    • 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
      • +
    • Todd Pihl, Fredrick National Laboratory for Cancer Research
    From 23fe458c9e472ec17e6cc4e9829ba15029a91da1 Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Tue, 18 Aug 2020 10:56:44 -0400 Subject: [PATCH 14/50] hyperlink logo --- index.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index.html b/index.html index 8132bc88d..2155d6d0f 100644 --- a/index.html +++ b/index.html @@ -19,7 +19,7 @@

    DATA4MICCAI

    A MICCAI 2020 Tutorial

    - Italian Trulli + MICCAI 2020
    From c9c6ecc40784a89abdbc7853cd6b6b73bd8081f7 Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Tue, 18 Aug 2020 12:04:28 -0400 Subject: [PATCH 15/50] remove education --- index.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index.html b/index.html index 2155d6d0f..894b28819 100644 --- a/index.html +++ b/index.html @@ -23,7 +23,7 @@

    A MICCAI 2020 Tutorial

    -

    Public Cancer Imaging Data Repositories for Biomedical Data Science Research and Education

    +

    Public Cancer Imaging Data Repositories for Biomedical Data Science Research

    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.

    From 1bd6056fd0c32f69794cb8429f26e65325bf743b Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Tue, 18 Aug 2020 12:17:59 -0400 Subject: [PATCH 16/50] update readme --- README.md | 14 +++----------- 1 file changed, 3 insertions(+), 11 deletions(-) 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. From c64188e807030b7a156a0bd2c3a4a0704ebfafcc Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Wed, 19 Aug 2020 14:52:42 -0400 Subject: [PATCH 17/50] add organizers --- index.html | 2 ++ 1 file changed, 2 insertions(+) diff --git a/index.html b/index.html index 894b28819..38059035d 100644 --- a/index.html +++ b/index.html @@ -65,6 +65,8 @@

    Organizers

  7. John Freymann, Fredrick National Laboratory for Cancer Research
  8. Justin Kirby, Fredrick National Laboratory for Cancer Research
  9. Todd Pihl, Fredrick National Laboratory for Cancer Research
    10. +
  10. Fred Prior, University of Arkansas Medical School
    11. +
  11. Lawrence Tarbox, University of Arkansas Medical School
    12. From 7a9f63990c92213a66d10dc17cc551883c05e168 Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Fri, 21 Aug 2020 16:31:52 -0400 Subject: [PATCH 18/50] updates --- index.html | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/index.html b/index.html index 38059035d..3c7be324a 100644 --- a/index.html +++ b/index.html @@ -3,7 +3,7 @@ - DICOM4MICCAI: Public Cancer Imaging Data Repositories for Biomedical Data Science Research + DATA4MICCAI: Public Cancer Imaging Data Repositories for Biomedical Data Science Research @@ -67,6 +67,9 @@

    Organizers

  12. Todd Pihl, Fredrick National Laboratory for Cancer Research
  13. Fred Prior, University of Arkansas Medical School
  14. Lawrence Tarbox, University of Arkansas Medical School
    15. +
  15. Bill Longabaugh, Institute for Systems Biology
    16. +
  16. David Pot, General Dynamics IT
    17. +
  17. Ron Kikinis, Brigham and Women's Hospital / Harvard Medical School
    18. From dd0daedbcc3b4c610c45beb9c96ae2a725254c4d Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Tue, 1 Sep 2020 10:32:56 -0400 Subject: [PATCH 19/50] update schedule --- index.html | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/index.html b/index.html index 3c7be324a..a74c683a1 100644 --- a/index.html +++ b/index.html @@ -41,7 +41,9 @@

    Public Cancer Imaging Data Repositories for Biomedical Data Science Research

    Preliminary agenda

    -

    Session 1: TCIA

    +

    Overall introduction

    + +

    Session 1: TCIA

    • introduction | 10 min
      • From eb215e546c5b26bf92dbac848fc77d6675f1a8cd Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Tue, 1 Sep 2020 10:34:59 -0400 Subject: [PATCH 20/50] update agenda --- index.html | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/index.html b/index.html index a74c683a1..749cb31be 100644 --- a/index.html +++ b/index.html @@ -51,12 +51,17 @@

      Session 1: TCIA

    • TCIA hands-on demo | 45 min
    +

    Coffee break | 15 min

    +

    Session 2: IDC

    • introduction | 10 min
    • IDC presentation | 20 min
      • -
    • IDC hands-on demo | 45 min
      • +
    • IDC hands-on demo - part 1| 20 min
      • +
    • Q&A | 10 min
      • +
    • IDC hands-on demo - part 2| 20 min
      • +
    • Q&A | 10 min

    Organizers

    From 8bf65b086265c9cd0c03670b63dedbea1c3dbbf2 Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Tue, 1 Sep 2020 10:36:14 -0400 Subject: [PATCH 21/50] styling --- index.html | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/index.html b/index.html index 749cb31be..c94b75985 100644 --- a/index.html +++ b/index.html @@ -58,9 +58,9 @@

    Session 2: IDC

    • introduction | 10 min
    • IDC presentation | 20 min
      • -
    • IDC hands-on demo - part 1| 20 min
      • +
    • IDC hands-on demo - part 1 | 20 min
    • Q&A | 10 min
      • -
    • IDC hands-on demo - part 2| 20 min
      • +
    • IDC hands-on demo - part 2 | 20 min
    • Q&A | 10 min
    From c0054ef27514a9333778b7289f78ce88abccd5a1 Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Tue, 1 Sep 2020 10:40:04 -0400 Subject: [PATCH 22/50] refinement --- index.html | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/index.html b/index.html index c94b75985..a61a47f00 100644 --- a/index.html +++ b/index.html @@ -41,9 +41,9 @@

    Public Cancer Imaging Data Repositories for Biomedical Data Science Research

    Preliminary agenda

    -

    Overall introduction

    +

    Overall introduction | 15 min

    -

    Session 1: TCIA

    +

    Session 1: TCIA | 1 hr 30 min

    • introduction | 10 min
      • @@ -53,7 +53,7 @@

      Session 1: TCIA

      Coffee break | 15 min

      -

      Session 2: IDC

      +

      Session 2: IDC | 1 hr 30 min

      • introduction | 10 min
        • @@ -63,6 +63,8 @@

        Session 2: IDC

      • IDC hands-on demo - part 2 | 20 min
      • Q&A | 10 min
      + +

      Wrap-up | 15 min

      Organizers

      From f8f9890ccffa0ef2322e835a94c1f68af029b0ad Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Tue, 1 Sep 2020 10:43:18 -0400 Subject: [PATCH 23/50] add more details --- index.html | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/index.html b/index.html index a61a47f00..c0bc1e381 100644 --- a/index.html +++ b/index.html @@ -41,12 +41,12 @@

      Public Cancer Imaging Data Repositories for Biomedical Data Science Research

      Preliminary agenda

      -

      Overall introduction | 15 min

      +

      Overall introduction - Keyvan Farahani | 15 min

      Session 1: TCIA | 1 hr 30 min

        -
      • introduction | 10 min
        • +
      • Introduction - John Freymann | 10 min
      • TCIA presentation | 20 min
      • TCIA hands-on demo | 45 min
      @@ -56,7 +56,7 @@

      Coffee break | 15 min

      Session 2: IDC | 1 hr 30 min

        -
      • introduction | 10 min
        • +
      • Introduction - Todd Pihl | 10 min
      • IDC presentation | 20 min
      • IDC hands-on demo - part 1 | 20 min
      • Q&A | 10 min
        • From 7eb2e13efc1a5aa9e57af36ebb1a9ea6dec003fe Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Tue, 1 Sep 2020 10:49:44 -0400 Subject: [PATCH 24/50] update agenda --- index.html | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/index.html b/index.html index c0bc1e381..4c32df652 100644 --- a/index.html +++ b/index.html @@ -47,10 +47,14 @@

        Session 1: TCIA | 1 hr 30 min

        • Introduction - John Freymann | 10 min
          • -
        • TCIA presentation | 20 min
          • -
        • TCIA hands-on demo | 45 min
          • +
        • Publishing data - John Freymann | 10 min
          • +
        • Browsing Rad/Path Data - Justin Kirby | 20 min
          • +
        • Searching/filtering/displaying data - Lawrence Tarbox | 30 min
          • +
        • Additional tools to access the data - Fred Prior | 10 min
          • +
        • Miscellaneous - Fred Prior | 5 min
          • +
        • Q&A - Fred Prior | 5 min
        - +

        Coffee break | 15 min

        Session 2: IDC | 1 hr 30 min

        @@ -64,7 +68,7 @@

        Session 2: IDC | 1 hr 30 min

      • Q&A | 10 min
      -

      Wrap-up | 15 min

      +

      Summary and wrap-up - Keyvan Farahani | 15 min

      Organizers

      From ec3e210a7a8b8ffb8f4475e22af4e860da1c5bae Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Tue, 1 Sep 2020 10:52:57 -0400 Subject: [PATCH 25/50] agenda updates --- index.html | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/index.html b/index.html index 4c32df652..4aa4f9c12 100644 --- a/index.html +++ b/index.html @@ -43,7 +43,7 @@

      Preliminary agenda

      Overall introduction - Keyvan Farahani | 15 min

      -

      Session 1: TCIA | 1 hr 30 min

      +

      Session 1: The Cancer Imaging Archive (TCIA) | 1 hr 30 min

      • Introduction - John Freymann | 10 min
        • @@ -57,11 +57,11 @@

        Session 1: TCIA | 1 hr 30 min

        Coffee break | 15 min

        -

        Session 2: IDC | 1 hr 30 min

        +

        Session 2: Imaging Data Commons (IDC) | 1 hr 30 min

          -
        • Introduction - Todd Pihl | 10 min
          • -
        • IDC presentation | 20 min
          • +
        • Introduction to NCI Cancer Research Data Commons (CRDC) - Todd Pihl | 10 min
          • +
        • Introduction to IDC | 20 min
        • IDC hands-on demo - part 1 | 20 min
        • Q&A | 10 min
        • IDC hands-on demo - part 2 | 20 min
          • From cb722fa169a6c975ca1a91a6f76d728721e1ec82 Mon Sep 17 00:00:00 2001 From: Keyvan Farahani <38476531+farahank@users.noreply.github.com> Date: Tue, 8 Sep 2020 22:11:36 -0400 Subject: [PATCH 26/50] Update index.html Updated timeline following the shortened version of the tutorial (2 hr. total) -KF --- index.html | 27 ++++++++++++--------------- 1 file changed, 12 insertions(+), 15 deletions(-) diff --git a/index.html b/index.html index 4aa4f9c12..c8358ffca 100644 --- a/index.html +++ b/index.html @@ -41,34 +41,31 @@

          Public Cancer Imaging Data Repositories for Biomedical Data Science Research

          Preliminary agenda

          -

          Overall introduction - Keyvan Farahani | 15 min

          +

          Overall introduction - Keyvan Farahani | 5 min

          -

          Session 1: The Cancer Imaging Archive (TCIA) | 1 hr 30 min

          +

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

            -
          • Introduction - John Freymann | 10 min
            • -
          • Publishing data - John Freymann | 10 min
            • -
          • Browsing Rad/Path Data - Justin Kirby | 20 min
            • -
          • Searching/filtering/displaying data - Lawrence Tarbox | 30 min
            • +
          • Introduction - John Freymann | 5 min
            • +
          • Publishing data - John Freymann | 5 min
            • +
          • Browsing Rad/Path Data - Justin Kirby | 10 min
            • +
          • Searching/filtering/displaying data - Lawrence Tarbox | 15 min
          • Additional tools to access the data - Fred Prior | 10 min
            • -
          • Miscellaneous - Fred Prior | 5 min
          • Q&A - Fred Prior | 5 min
          -

          Coffee break | 15 min

          +

          Coffee break | 10 min

          -

          Session 2: Imaging Data Commons (IDC) | 1 hr 30 min

          +

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

            -
          • Introduction to NCI Cancer Research Data Commons (CRDC) - Todd Pihl | 10 min
            • +
          • Introduction to NCI Cancer Research Data Commons (CRDC) - Todd Pihl | 5 min
          • Introduction to IDC | 20 min
            • -
          • IDC hands-on demo - part 1 | 20 min
            • -
          • Q&A | 10 min
            • -
          • IDC hands-on demo - part 2 | 20 min
            • -
          • Q&A | 10 min
            • +
          • IDC hands-on demo | 20 min
            • +
          • Q&A - | 5 min
          -

          Summary and wrap-up - Keyvan Farahani | 15 min

          +

          Summary and wrap-up - Keyvan Farahani | 10 min

          Organizers

          From a1c04bac9eebe68d5a128119564e9ebd70e87497 Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Wed, 9 Sep 2020 09:46:53 -0400 Subject: [PATCH 27/50] more updates --- index.html | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/index.html b/index.html index c8358ffca..2cd549abd 100644 --- a/index.html +++ b/index.html @@ -60,9 +60,9 @@

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

          • Introduction to NCI Cancer Research Data Commons (CRDC) - Todd Pihl | 5 min
            • -
          • Introduction to IDC | 20 min
            • -
          • IDC hands-on demo | 20 min
            • -
          • Q&A - | 5 min
            • +
          • Introduction to IDC - Andrey Fedorov | 20 min
            • +
          • IDC hands-on demo - Andrey Fedorov | 20 min
            • +
          • Q&A - Andrey Fedorov | 5 min

          Summary and wrap-up - Keyvan Farahani | 10 min

          From aae8be8ec03d5b22a3b8aada7ae9b59a9c7affb3 Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Tue, 15 Sep 2020 10:30:50 -0400 Subject: [PATCH 28/50] add date/time --- index.html | 3 +++ 1 file changed, 3 insertions(+) diff --git a/index.html b/index.html index 2cd549abd..17584a580 100644 --- a/index.html +++ b/index.html @@ -24,6 +24,9 @@

          A MICCAI 2020 Tutorial

          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.

          From f911d4aa8fd27fb5e65e37da55c6f3bad761666e Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Wed, 23 Sep 2020 16:54:52 -0400 Subject: [PATCH 29/50] change break to be 15 minutes --- index.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index.html b/index.html index 17584a580..15d61f655 100644 --- a/index.html +++ b/index.html @@ -57,7 +57,7 @@

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

        • Q&A - Fred Prior | 5 min
        -

        Coffee break | 10 min

        +

        Coffee break | 15 min

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

        From a70b07ce44c3ec6d96ea063993d2c3927a1ba5ee Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Fri, 25 Sep 2020 20:51:49 -0400 Subject: [PATCH 30/50] update schedule --- index.html | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/index.html b/index.html index 15d61f655..a6dc9a13c 100644 --- a/index.html +++ b/index.html @@ -64,7 +64,8 @@

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

        • Introduction to NCI Cancer Research Data Commons (CRDC) - Todd Pihl | 5 min
        • Introduction to IDC - Andrey Fedorov | 20 min
          • -
        • IDC hands-on demo - Andrey Fedorov | 20 min
          • +
        • IDC hands-on demo: IDC Portal - Andrey Fedorov | 10 min
          • +
        • IDC hands-on demo: IDC Cohorts - Andrey Fedorov | 10 min
        • Q&A - Andrey Fedorov | 5 min
        From 94bd8082b587c63550f31462d99b43b11e7bf5a4 Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Thu, 1 Oct 2020 13:35:11 -0400 Subject: [PATCH 31/50] remove preliminary --- index.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index.html b/index.html index a6dc9a13c..68abed622 100644 --- a/index.html +++ b/index.html @@ -42,7 +42,7 @@

        Time: 10 am EST (2 pm UTC)

      • To be able to search for and identify imaging collections of interest and prepare them for further analysis.
-

Preliminary agenda

+

Agenda

Overall introduction - Keyvan Farahani | 5 min

From 6fde7fad1f9c81c7816512d42cb625efc139ca7f Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Thu, 8 Oct 2020 16:26:58 -0400 Subject: [PATCH 32/50] add links to videos --- index.html | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/index.html b/index.html index 68abed622..6ac13ebdb 100644 --- a/index.html +++ b/index.html @@ -63,9 +63,9 @@

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

  • Introduction to NCI Cancer Research Data Commons (CRDC) - Todd Pihl | 5 min
    • -
  • Introduction to IDC - Andrey Fedorov | 20 min
    • -
  • IDC hands-on demo: IDC Portal - Andrey Fedorov | 10 min
    • -
  • IDC hands-on demo: IDC Cohorts - Andrey Fedorov | 10 min
    • +
  • Introduction to IDC - Andrey Fedorov | 20 min [video]
    • +
  • IDC hands-on demo: IDC Portal - Andrey Fedorov | 10 min [video]
    • +
  • IDC hands-on demo: IDC Cohorts - Andrey Fedorov | 10 min [video]
  • Q&A - Andrey Fedorov | 5 min
From 5e87e56ce3999a0712158dbc5b5bd36b1c6f6a8d Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Sun, 15 Nov 2020 17:56:59 -0500 Subject: [PATCH 33/50] add Todd's presentation --- index.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index.html b/index.html index 6ac13ebdb..d8129ed99 100644 --- a/index.html +++ b/index.html @@ -62,7 +62,7 @@

Coffee break | 15 min

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

    -
  • Introduction to NCI Cancer Research Data Commons (CRDC) - Todd Pihl | 5 min
    • +
  • Introduction to NCI Cancer Research Data Commons (CRDC) - Todd Pihl | 5 min,a href="https://youtu.be/aPfqZIHsBQk">[video]
  • Introduction to IDC - Andrey Fedorov | 20 min [video]
  • IDC hands-on demo: IDC Portal - Andrey Fedorov | 10 min [video]
  • IDC hands-on demo: IDC Cohorts - Andrey Fedorov | 10 min [video]
    • From bcae9e2d6b6f4ea3575666b2308810066781363b Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Sun, 15 Nov 2020 18:12:51 -0500 Subject: [PATCH 34/50] fix typo --- index.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index.html b/index.html index d8129ed99..e83896cef 100644 --- a/index.html +++ b/index.html @@ -62,7 +62,7 @@

    Coffee break | 15 min

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

      -
    • Introduction to NCI Cancer Research Data Commons (CRDC) - Todd Pihl | 5 min,a href="https://youtu.be/aPfqZIHsBQk">[video]
      • +
    • Introduction to NCI Cancer Research Data Commons (CRDC) - Todd Pihl | 5 min [video]
    • Introduction to IDC - Andrey Fedorov | 20 min [video]
    • IDC hands-on demo: IDC Portal - Andrey Fedorov | 10 min [video]
    • IDC hands-on demo: IDC Cohorts - Andrey Fedorov | 10 min [video]
      • From 61b6c2b0dd028b46821c0b4fb2eb1766ebf46d4e Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Wed, 12 May 2021 18:13:06 -0400 Subject: [PATCH 35/50] update to 2021 content --- index.html | 92 +++++++++++++++++++--------------------------- index_2020.html | 97 +++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 135 insertions(+), 54 deletions(-) create mode 100644 index_2020.html diff --git a/index.html b/index.html index e83896cef..465a69d38 100644 --- a/index.html +++ b/index.html @@ -3,7 +3,7 @@ - DATA4MICCAI: Public Cancer Imaging Data Repositories for Biomedical Data Science Research + DATA4MICCAI: NIH Cancer Imaging Data Repositories for Biomedical Data Science Research @@ -17,73 +17,57 @@

      DATA4MICCAI

      -

      A MICCAI 2020 Tutorial

      +

      A MICCAI 2021 Tutorial

      - MICCAI 2020 + MICCAI 2020
      -

      Public Cancer Imaging Data Repositories for Biomedical Data Science Research

      +

      NIH 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. -
      +

      Date: TBD

      +

      Time: TBD

      +
      + 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.

      Agenda

      -

      Overall introduction - Keyvan Farahani | 5 min

      - -

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

      - -
        -
      • Introduction - John Freymann | 5 min
        • -
      • Publishing data - John Freymann | 5 min
        • -
      • Browsing Rad/Path Data - Justin Kirby | 10 min
        • -
      • Searching/filtering/displaying data - Lawrence Tarbox | 15 min
        • -
      • Additional tools to access the data - Fred Prior | 10 min
        • -
      • Q&A - Fred Prior | 5 min
        • -
      - -

      Coffee break | 15 min

      - -

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

      - -
        -
      • Introduction to NCI Cancer Research Data Commons (CRDC) - Todd Pihl | 5 min [video]
        • -
      • Introduction to IDC - Andrey Fedorov | 20 min [video]
        • -
      • IDC hands-on demo: IDC Portal - Andrey Fedorov | 10 min [video]
        • -
      • IDC hands-on demo: IDC Cohorts - Andrey Fedorov | 10 min [video]
        • -
      • Q&A - Andrey Fedorov | 5 min
        • -
      - -

      Summary and wrap-up - Keyvan Farahani | 10 min

      +

      TBD

      Organizers

      • 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
        • -
      • Todd Pihl, 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
        • -
      • David Pot, General Dynamics IT
        • -
      • Ron Kikinis, 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
      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

      + +
        +
      • Introduction - John Freymann | 5 min
        • +
      • Publishing data - John Freymann | 5 min
        • +
      • Browsing Rad/Path Data - Justin Kirby | 10 min
        • +
      • Searching/filtering/displaying data - Lawrence Tarbox | 15 min
        • +
      • Additional tools to access the data - Fred Prior | 10 min
        • +
      • Q&A - Fred Prior | 5 min
        • +
      + +

      Coffee break | 15 min

      + +

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

      + +
        +
      • Introduction to NCI Cancer Research Data Commons (CRDC) - Todd Pihl | 5 min [video]
        • +
      • Introduction to IDC - Andrey Fedorov | 20 min [video]
        • +
      • IDC hands-on demo: IDC Portal - Andrey Fedorov | 10 min [video]
        • +
      • IDC hands-on demo: IDC Cohorts - Andrey Fedorov | 10 min [video]
        • +
      • Q&A - Andrey Fedorov | 5 min
        • +
      + +

      Summary and wrap-up - Keyvan Farahani | 10 min

      + +

      Organizers

      + +
        +
      • 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
        • +
      • Todd Pihl, 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
        • +
      • David Pot, General Dynamics IT
        • +
      • Ron Kikinis, Brigham and Women's Hospital / Harvard Medical School
        • +
      + +
      + +
      + + + From 79c7ec42e410995a4a4fd0f393ebf7db6043db7c Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Wed, 12 May 2021 18:14:59 -0400 Subject: [PATCH 36/50] add breaks --- index.html | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/index.html b/index.html index 465a69d38..dd3167c23 100644 --- a/index.html +++ b/index.html @@ -27,14 +27,14 @@

      NIH Cancer Imaging Data Repositories for Biomedical Data Science ResearchDate: TBD

      Time: TBD

      -
      +

      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 @@ -45,7 +45,7 @@

      Time: TBD

      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. From 10dd4cae4aa1d04d575eca6dec74fe65c64c6a93 Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Wed, 12 May 2021 18:16:12 -0400 Subject: [PATCH 37/50] add pointer to previous edition --- index.html | 3 +++ 1 file changed, 3 insertions(+) diff --git a/index.html b/index.html index dd3167c23..c3d8dd59d 100644 --- a/index.html +++ b/index.html @@ -71,6 +71,9 @@

      Organizers

+ + MICCAI 2020 tutorial page +