Skip to end of metadata
Go to start of metadata

Topics on this page describe how to search the local and remote image databases for images.

You can print and export wiki pages.

Topics in this chapter include:

Introduction to the TCIA Data Portal

TCIA Data Portal enables you to search for images in the local TCIA in vivo image repository. If available, you can also search remote imaging archives.

TCIA submissions are organized in the following hierarchy, which is important to remember in creating your search query and reviewing search results:

Collection > Patient (Subject) > Study > Series > Images

In other words, a Collection is the largest organizing concept within TCIA and it includes data about Patients (also called Subjects). As you continue to drill down to more granular concepts, Patients contain Studies, Studies contain (Image) Series, and Series contain individual Images.

Return to top of page

Logging In

You can search and download public data without logging in to the TCIA Data Portal. To access restricted data, however, you must log in first to see that data in your search results.

  1. In the top menu bar, click Login Button.
    The Login window appears.
    Login window
  2. Enter your user name and password, then click Log In.

Browser Support

TCIA supports the latest versions of Google Chrome and Mozilla Firefox browsers.

Searching for Image Studies

TCIA provides two ways to search for image studies:

When you first open TCIA Data Portal, the Summary tab displays filters for a simple search and pie charts.

TCIA Simple Search page

Click one or more boxes next to each search filter to select it. As you select search filters, they move to the top of the list. They also appear in Boolean query format above the pie charts. This query specifies the filters you have applied to your search. Click Clear if you want to remove all of your filters at once and start over. You can save your query as a URL for later use or to put in an email to a colleague. For more information about sharing, go to Sharing a Query.

You can filter (narrow) your search by Collections, Image Modality, Anatomical Site, Date released on TCIA, and Subject IDs. You can also specify the minimum number of image studies you want to match each search filter. For Collections, if you know the name of the collection, click Magnifying glass icon to enter it instead of finding and clicking the collection's box.

The Simple Search page shows a summary of image studies that match your search criteria. Your selections appear in the following ways:

  • Boxes you selected are checked.
  • Pie charts update to show the exact search results.
  • Breadcrumb-style labels at the top of the page show the applied search filters (not all may display due to space constraints).
  • Count of search results appears.

Simple Search tab showing selections and summary of search results

The pie charts show the count of image studies in your search results by Collection, Image Modality, and Anatomical Site. Click a pie slice or hover over it to see the name of the Collection, Image Modality, or Anatomical Site, and number of each, in your search results.

Count by Collections with selected search filter and filter name

The Search Results tab shows the same results as the pie charts but in tabular form.

Search Results in tabular form

Text searches involve entering any text that might appear in any search filter.

Text Search tab with Text Search box within it

Results are displayed in pie charts and a table, just as with the simple search.

Performing a Simple Search

A simple search allows you to search for image studies based on a combination of the following search filters: Collections, Image Modality, Anatomical Site, Date released on TCIA, and Subject IDs. The more criteria you select, the fewer results you receive. After you select your search criteria, you can save your query to use later.

To perform a simple search

  1. On the TCIA home page, click the Simple Search tab.
    The Simple Search page appears.
    TCIA Simple Search page
  2. Select filters to narrow down the available image series.

    To SelectDo This
    Collections

    Option 1: Click the box next to each collection name you want to select.

    4D-Lung Collection selected


    Option 2: Click the magnifying glass to enter a name.
    Collections filter

    Image Modality

    Option 1: Click the box next to one or more image modalities.
    If you select more than one image modality, clicking ANY will returns any study that is associated with any of the modalities you selected. Clicking ALL returns all studies that are associated with all of the modalities you selected.

    Checklist of image modalities with CT selected

    Anatomical Site

    Option 1: Click the box next to each anatomical site you want to select.

    Checklist of anatomical sites

    At least X time point (DICOM studies)

    Enter the minimum number of time points that match the criteria of your search. This filter allows you to see subjects that have more than one DICOM study (that is, the patient was seen at multiple time points).

    At least X (number) time point (DICOM studies) field

    Date released on TCIA

    Enter a From and To date to narrow your search results to studies that TCIA first made available during that date range.

    Alternately, select the Apply "Available" date range box to exclude studies that were unavailable to TCIA during the selected date range.

    Date released on TCIA

    Subject IDs

    Enter Subject IDs associated with the image series you want to receive in your search results. Separate each Subject ID with a comma and then click Apply Subject IDs.

    Subject IDs text box

    The Summary tab shows updated pie charts and the number of image series in the search results.
    Summary tab showing pie charts
    Click the Search Results tab for more detailed results.


Return to top of page

Performing a Text Search

  1. Open the Text Search tab.
    Text Search tab
  2. Enter text from any of the search filters into the Text Search box and click Search button.
    Image series matching your search text appears in the Search Results.
    Text search results

Viewing Subject Details

The search results from your query are presented both on the Summary tab in pie charts and on the Search Results tab in a table. Each record in the table corresponds to one subject (patient) and displays the collection(s), study(ies), and image series associated with that subject.

From the Search Results tab, you can view subject details, view all image series associated with the subject, and add image series to your cart for download. You can also view the DICOM header for a selected image series. In the future, you will be able to view the image.

To view subject details

  1. Search for studies that match criteria that interest you.
    The Summary tab refreshes to show your search results in pie chart form.
  2. Click the Search Results tab.
    The search results that match your criteria appear sorted by Subject ID.

    Search results table
    You can now add all studies associated with a subject to your cart at the same time or drill down to an individual study and add it to your cart instead.

  3. Click a Subject ID link.
    All studies associated with this subject appear. In this example, this subject is only associated with one study, and only one image series is associated with that study.
    Subject details for selected subject, showing four studies

    The red asterisk indicates that the date, which is the date that this series was first available at TCIA, has been offset to protect private health information.

  4. Click the arrow to the left of the cart icon to view details about the selected study.
    All of the image series associated with that study appear.
    Details about selected series
    You can now

Viewing Thumbnails of the Image Series

You can view thumbnails of all images in the selected series and then open selected images for further analysis in another image system.

To view thumbnails

  1. View the details for a subject.
  2. Select a study and view its details.
  3. In the row for an image series, click Magnifying glass.
    Image series for a selected subject
    Thumbnails of all of the images in the selected image series appear.

    Thumbnails of all images in a selected image series
  4. Click any image to download it to your computer. 
    Follow your browser's instructions to open or save the file.
    File downloaded to Chrome, Show All button

Viewing DICOM Data

Digital Imaging and Communications in Medicine (DICOM) is a standard for handling, storing, printing, and transmitting information in medical imaging.

You can view the DICOM tags that form the header of the selected image series.

To view DICOM data

  1. View the details for a subject.
  2. Select a study and view its details.
  3. In the row for an image series, click DICOM button.
    The DICOM tags associated with the image series appear.
    DICOM Tags for Image

Downloading Study Data

You can download items you add during the current work session. Before you download items you must download and then install the NBIA Data Retriever.

You select items to download by first searching for them in TCIA and then adding them to your cart.

Adding Data to the Cart

Your cart is a holding place for data you have selected to download. You can add all image series associated with a subject, all image series associated with a study, or one or more selected image series to your cart. 

To add all image series associated with a subject to the cart

  1. Search for the subject.
  2. Click the Search Results tab.
  3. Click the cart icon in the row of one or more subjects.
    The cart icon turns green and the number of image series now in your cart appears next to the cart. The cart itself, in the upper-right of the window, shows how many image series are in it and how large the download will be.

    To remove all of the data associated with this subject from the cart, click the cart icon again.


    Search results tab showing all image series associated with the subject selected

To add all image series associated with a study to the cart

  1. Search for the subject.
  2. Click the Search Results tab.
  3. Click a Subject ID link.
    All of the studies associated with this subject appear.
  4. Click the cart icon next to one or more studies.
    All of the image series in the selected studies are added to the cart.

    • The cart icon in the study row turns green. If you did not select all of the studies associated with the subject, the cart icon in the subject row turns yellow.

    • The cart itself, in the upper-right of the window, shows how many image series are in it and how large the download will be.

      To remove all of the data associated with this subject from the cart, click the cart icon again.

      Search results tab showing two studies selected


To add one or more image series to the cart

  1. Search for the subject.
  2. Click the Search Results tab.
  3. Click a Subject ID link to open all series associated with that subject.
  4. Click the cart icon for one or more series.
    The cart icon you select turns green.
    The cart icon for the subject turns yellow, indicating that you have not selected all available series for this subject.
    Search results tab showing one image series selected

Downloading the NBIA Data Retriever


Get the Downloader App

Click one of the following links to download the NBIA Data Retriever for that operating system.

  • DEB (tested on Ubuntu)
    To run this file, type the following at the command prompt:
    sudo -S dpkg -r tciadownloader;sudo -S dpkg -i nbia-data-retriever-3.2.deb

After you search for images of interest and add them to your data basket, you can download them.

The most convenient method of downloading is by using the NBIA Data Retriever. You must install the NBIA Data Retriever before you begin downloading. You only have to install it once to use it in future downloading sessions.

Consult the NBIA Data Retriever FAQ for more information about NBIA Data Retriever versions and usage.

Installing the NBIA Data Retriever

To install the NBIA Data Retriever on Windows

  1. Download the installer package for Windows using the Windows link above.
  2. Save the installer package file to your computer.
  3. Install the app by double-clicking the installer package file.
  4. Agree to the terms in the License Agreement and click Install.
  5. When the Setup Wizard ends, click Finish.

To install the NBIA Data Retriever on Mac

The Mac version of the NBIA Data Retriever is only available through the iOS App Store. It requires a manifest file to work. You can download the app first or create a manifest file first. If you download the app first, right-click the manifest file and select Open With Downloader App. If you create a manifest file first, right-click it and select Open With App Store. This installs the app and then opens the manifest file in the app.

  1. On your Mac, find the NBIA Data Retriever on the Mac App Store.

    The NBIA Data Retriever is free but still requires you to log in to download it. Consider changing your iOS Password Settings so that you can download free software without having to log in separately for it.

  2. Click Get, then click Install App. The NBIA Data Retriever is free.
    The app starts downloading to your Mac. When the download is complete, you can open a manifest file with the NBIA Data Retriever.

To install the NBIA Data Retriever on Linux (centOS or Ubuntu)

You must have the sudo privilege on your computer and a sudo password to install the NBIA Data Retriever on CentOS and Ubuntu.

  1. Download the installer package for centOS or Ubuntu using the links above.
  2. Save the installer package file to your computer.
  3. Open a command window and go to the location where you saved the installer.
  • For a centOS system, enter the following at the command prompt:
    sudo yum -v -y remove Downloader.x86_64;sudo yum -y install downloader-3.2-1.x86_64.rpm
  • For a Ubuntu system, enter the following at the command prompt:
    sudo -S dpkg -r Downloader;sudo -S dpkg -i downloader-3.2.deb
    Enter the sudo password when prompted.

Downloading Images Using the NBIA Data Retriever

When you download images you have added to your cart, TCIA provides a list of these images in a manifest file (manifest-xxx.tcia). You must have already installed the NBIA Data Retriever to open this manifest file and download the images.

To download images using the NBIA Data Retriever

  1. Search for images of interest.
  2. Add those images to your cart.
  3. Click the cart icon in the top-right of the page Cart icon.
    The cart contents appear.
    Cart contents showing three image series ready to be downloaded
  4. Click Download button.
    A message appears reminding you to download the NBIA Data Retriever. If you have already downloaded it, click Do not show this message again and click Download button. Otherwise, click Get NBIA Data Retriever App Button to go to a page with links for downloads for each operating system.
    Message box prompting you to download the NBIA Data Retriever
  5. Open the manifest-xxx.tcia file.
    The  NBIA Data Retriever appears, with the items you added to your cart in the Downloads table.
    NBIA Data Retriever in the process of downloading data

    The NBIA Data Retriever lists all items you selected in the cart. You can hover your mouse over the Patient ID, Study Instance, and Series Instance columns to reveal the complete corresponding IDs. You can also resize a column by selecting and dragging the column border.

    If you do not want to download any of those items, select them in the Downloads table and then click Delete. When you remove an item from the Downloads table, it stays in your cart.

  6. Click Browse to navigate to the destination where you want the images/annotations to be downloaded.

  7. Click Start to begin the download. You can monitor the download in the Progress column. The Status column indicates when the download for each item is complete.

    At any point in the process, you can click the Pause and Resume buttons to temporarily stop and restart the process.

    Note that files downloaded this way are not compressed. The downloaded files are stored in a child folder under the destination folder such as Collection Name > Patient ID > part of Study Date + part of Study ID + part of Study Description + last 5 digits of Study Instance UID > part of Series Number + part of Series Description + last 5 digits of Series Instance UID.

    Network Error?

    If network errors occur during large downloads, the NBIA Data Retriever retries downloading the series in the manifest file the number of times that your administrator has configured. The default is four times.

    After the automatic retries, you have the option of saving an error report, which you can share with the TCIA help desk, or of retrying just the failed series.

    NBIA Data Retriever download in progress with errors

Creating Manifest Files

You can create a manifest file in several ways:

Creating a Manifest File Using TCIA

To use the NBIA Data Retriever, you must already have a manifest file that lists the files you want to download. You create the manifest file by searching the data portal of The Cancer Imaging Archive. After installing the NBIA Data Retriever, double-click this manifest file to invoke the application.

Double-clicking the NBIA Data Retriever icon alone does not invoke the NBIA Data Retriever.

To create a manifest file:

  1. Search for images of interest.
  2. Add those images to your cart.
  3. Download images using the NBIA Data Retriever.
    A manifest file is created and downloaded to your computer. 
    • If you have already installed the NBIA Data Retriever, double-click the manifest file to open it using the NBIA Data Retriever. Click Open when your web browser prompts you to open the file. 
    • If you want to use this manifest file to download images more than once or download images you select on other machines, click Save at the web browser prompt. You can then double-click the saved manifest file in Windows Explorer on Windows, Finder on Mac, or File Manager on Linux to invoke the NBIA Data Retriever.

Creating a Manifest File Using the Manifest API

Refer to the Manifest API documentation for instructions on how to use the API. The outcome of the REST API call must be saved as a text file with the extension .tcia. 

Example Manifest Query 

curl -H "Authorization:Bearer d98c390f-b53d-4456-beb3-110e63663762" -k "http://localhost:8080/nbia-api/services/getManifestTextV2" -d "list=1.3.6.1.4.1.9328.50.3.336&includeAnnotation=false"

The API returns text that can be used as a manifest file for the NBIA Data Retriever.

downloadServerUrl=https://imaging-devcm.nci.nih.gov/nbia-download/servlet/DownloadServlet
includeAnnotation=false
noOfrRetry=4
databasketId=manifest-1523866570303.tcia
manifestVersion=3.0
ListOfSeriesToDownload=
1.3.6.1.4.1.9328.50.3.336

Creating a Manifest File Using the Shared List API

If you have a shared list, you can use the Shared List Query API to create a manifest file. Refer to the Shared List Query API documentation for instructions on how to use the API.

Example Manifest from Shared List Query 

curl -H "Authorization:Bearer a99171a1-b289-4700-9e4e-1bd73ce1bbb5" -k "http://localhost:8080/nbia-api/services/getManifestTextFromSharedList" -d "sharedList=scottslist&includeAnnotation=false"

The API returns text that can be used as a manifest file for the NBIA Data Retriever.

downloadServerUrl=https://imaging-devcm.nci.nih.gov/nbia-download/servlet/DownloadServlet
includeAnnotation=false
noOfrRetry=4
databasketId=manifest-1523866570303.tcia
manifestVersion=3.0
ListOfSeriesToDownload=
1.3.6.1.4.1.9328.50.3.336

Creating a Manifest File Using the JNLP Data Query API

If you have a JNLP file, you can use the JNLP Data Query API to create a manifest file. Refer to the JNLP Data Query API documentation for instructions on how to use the API.

Example Manifest from JNLP Data Query 

curl -H "Authorization:Bearer 3b2bf812-a97e-454e-af94-623b868a2955" -k "http://localhost:8080/nbia-api/services/getManifestFromJNLPFileData" -d "jnlpArgument=C:\Apps\nbia\apache-tomcat-7.0.68\temp\jnlp-data1521628213301.txt&includeAnnotation=false"

The API returns text that can be used as a manifest file for the NBIA Data Retriever.

downloadServerUrl=https://imaging-devcm.nci.nih.gov/nbia-download/servlet/DownloadServlet
includeAnnotation=false
noOfrRetry=4
databasketId=manifest-1523866570303.tcia
manifestVersion=3.0
ListOfSeriesToDownload=
1.3.6.1.4.1.9328.50.3.336


Sharing a Query

You can save your query for later use or share it with a colleague by email.

To share a query

  1. In the top menu bar, click Share button and then select Share my query.
    The Query URL box appears.

    Query URL message box that provides the URL you can share with others that contains your query
  2. Click Copy URL.
    The URL copies into your Clipboard.
  3. Paste the URL into an email or other document.

    Shared queries honor data permissions that may exist. Each person that runs the shared query will only see search results that he or she is allowed to see.

Sharing Data in Your Cart

Once you have added data to your cart, you can share it as a URL to a static set of data. When you or a colleague opens the URL in a browser window, the new TCIA Graphical User Interface (GUI) opens to the cart page. 

In the legacy TCIA data portal, this was called a shared list. This is a similar concept in the new TCIA GUI. 

To share data in your cart

  1. Add data to your cart.
  2. In the top menu bar, click Share button and then select Share My Cart.
    The Retrieve Cart Data URL box appears.

    Cart Data URL message box showing the URL where you can access or share your cart data
  3. Click Copy URL.
    The URL copies into your Clipboard.
  4. Paste the URL into an email or other document.

The shared cart honors data permissions that may exist. Each person that opens the shared cart will only see data that that person is allowed to see.

Return to top of page



  • No labels