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

You can print and export this user guide.

Introduction to the NBIA Data Portal

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

NBIA 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 NBIA 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.

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Browser Support

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

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Searching for Image Studies

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

NBIA provides two ways to search for image studies:

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

Summary page that displays after logging in

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, Species, Phantoms, 3rd-Party Analysis Results, Date Released, 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 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 page with filters, Collections, and Image Modalities

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 pie chart with Selected filter and Filter Name

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

Search results in tabular format

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

Text Search

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

Accessing Limited-Access Collections

You can search and download public data without logging in to the NBIA Data Portal. To access restricted data, however, you must log in first to see that data in your search results. Consult the TCIA Collections page to learn which collections have limited access.

  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.

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 NBIA home page, click the Simple Search tab. 
    The Simple Search page appears.
    Summary page that displays after logging in
  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

    Hovering over a collection name opens a window with information about the collection in it. Quickly move your mouse to this window, were you can select text and click links. The window stays open until you move your mouse away from it. 

    4D-Lung This data collection consists of images acquired during chemoradiotherapy of 20 locally-advanced, non-small cell lung cancer patients. The images include four-dimensional (4D) fan beam (4D-FBCT) and 4D cone beam CT (4D-CBCT). All patients underwent concurrent radiochemotherapy to a total dose of 64.8-70 Gy using daily 1.8 or 2 Gy fractions.  A single Radiation Oncologist delineated targets and organs at risk in all 4D-FBCT and a limited number of 4D-CBCT images. All patients underwent concurrent radiochemotherapy to a total dose of 64.8-70 Gy using daily 1.8 or 2 Gy fractions.  Please see the 4D-Lung wiki page to learn more about the images and to obtain any supporting metadata for this collection.


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

    Collections filter

    Image Modality

    Click the box next to one or more image modalities.

    If you select more than one image modality, clicking ANY 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.

    When you select the ANY search modifier here, only the studies that match your search criteria are returned. Be aware that these may be only be a subset of the studies belonging to a single subject (patient). The potential difference between total studies available and the number of studies returned by your search becomes clearer when you select the Total Studies and Total Series columns to appear in your search results. To do so, click at the top of the Search Results tab. Select Total Studies and Total Series in the Pick Columns list.

    Pick columns list of choices, which includes Cart, Collection ID, Subject ID, Studies, Total Studies, Series, and Total Series.


    Checklist of image modalities with CT selected

    Anatomical Site

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

    Checklist of anatomical sites

    Species

    Click the box next to the species you want your search results to represent, either human or Mus musculus (mouse).

    Phantoms

    Click the box next to the phantom option you want to select.

    Phantoms search filter. Options are Only Phantoms, Exclude Phantoms, and Include Phantoms.

    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

    3rd-Party Analysis Results

    3rd-party analysis results are derived data (e.g. segmentations) that were contributed by researchers who were not part of the group that originally submitted a collection to TCIA.

    Click the box next to each third-party analysis results option you want to select. Only DICOM data from third-party analysis results appear when using this search filter. A full listing of all third-party analysis data inclusive of non-DICOM formats can be found in the Analysis Results Directory.

    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

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

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

    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.

    Apply Subject IDs

  3. Select which columns you want to have appear in the detailed search results on the Search Results tab by clicking at the top of the Search Results tab. The Pick Columns panel appears. 

    Pick columns list of choices, which includes Cart, Collection ID, Subject ID, Studies, Total Studies, Series, and Total Series.

    Search results are shown in two different ways, as a summary and as detailed search results, and which one appears first matches your last choice. The Summary tab shows updated pie charts and the number of image series in the search results.

    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.

Performing a Text Search

A text search allows for searching of many of the database text fields, DICOM image tag data, and annotation files that are not available in the Simple search. Refer to the DICOM Data Dictionary for tags or field names you can use in a text search. A simple example of a text search is to find all subjects associated with the value pancreas by typing pancreas in the Text Search box. You can also use the field:searchTerm technique; for example, Body Part Examined:pancreas. In this example, the colon interprets the DICOM field from the value. Since text search also recognizes DICOM codes, you can also search on 0018,0015:pancreas, which is the DICOM code for Body Part Examined. Additionally, you can use a wildcard search such as Body Part Examined:panc* to find all subjects associated with values beginning with panc, including pancreas, pancreatic duct, and pancreatic duct and bile duct systems.

Text search does have some restrictions. These are:

  • The text string you use must have more than one character. The search won't return any values if the text string has only one character.
  • Do not use a forward slash (/) in your text string.
  • Do not use complex searches with AND or OR statements (text search supports Lucene syntax but only a single field can be searched at a time).

To perform a text search

  1. On the NBIA home page, click Text Search or Search Images > Text Search
    The Text Search page appears.

    Text Search tab with an empty text box, Clear button, and Search button

  2. Select the number of search results per page you want the search to return.
  3. In the box at the top of the page, enter a text string of two characters or more.
  4. Click Search button
    The search results appear.


Navigation Tips

  • Click the down arrow next to the Subject ID column header to sort the results alphabetically (A to Z or Z to A) by Subject ID.
  • Click the arrows at the bottom of the table to display the first, previous, next, or last page of results.
  • Click the page number links to move to a specific page of results.
  • In the Show (10) entries box in the bottom left, edit the default 10 to the number of entries you want to see on a search results page.
  • For performance Text Search will only return the first 3000 subjects that match the criteria

The following table describes each item in the search results table.

Search ResultDescription

Caret symbol and cart symbol

Click the caret to view the subject details. Click the cart symbol to add image series to your cart.
Collection IDCollection identifier
Subject ID

Click the Subject ID to view the details for all study images for this subject, a single series' thumbnails, or the DICOM header for the first image in the series.

Hit

The field in the study where the text string that you entered in the search criteria appears.

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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.
    A list of 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 Thumbnail icon.
    Access thumbnails with Thumbnail icon
    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 .
    The DICOM tags associated with the image series appear.
    DICOM Tags for Image

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Downloading NBIA Images

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 NBIA and then adding them to your cart.

The following topics are in this section:

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 NBIA Data Retriever

PlatformFileSize
Windows100.32 MB
Mac
Linux (tested on CentOS)

NBIADataRetriever-3.5-1.x86_64.rpm

To run this file, type the following at the command prompt:
sudo yum -v -y remove NBIADataRetriever -3.3-1.x86_64.rpm;sudo yum -y install NBIADataRetriever -3.5-1.x86_64.rpm

91.15 MB
Linux (tested on Ubuntu)

nbia-data-retriever-3.5.deb

To run this file, type the following at the command prompt:
sudo -S dpkg -r nbia-data-retriever-3.3.deb;sudo -S dpkg -i nbia-data-retriever-3.5.deb

82.8 MB

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 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 Mac 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 NBIA Data Retriever. 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 macOS 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 NBIADataRetriever-3.3-1.x86_64.rpm;sudo yum -y install NBIADataRetriever-3.5-1.x86_64.rpm
    • For an Ubuntu system, enter the following at the command prompt:
      sudo -S dpkg -r nbia-data-retriever-3.3.deb;sudo -S dpkg -i nbia-data-retriever-3.5.deb
      Enter the sudo password when prompted.

Downloading Images Using the NBIA Data Retriever

When you start downloading the images you have added to the data basket, NBIA provides a list of those 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.

  1. Search for images of interest.
  2. Add those images to your data basket.
  3. Open the My Data Basket page and click Start Download.
  4. Click the manifest-xxx.tcia file.
    If you are only downloading public images, the NBIA Data Retriever appears, listing the items in your data basket. If you are downloading any private images, see the section about downloading private data.
    NBIA Data Retriever in the process of downloading data

    The NBIA Data Retriever lists all items you selected in the data basket. 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 data basket.

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

  6. 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 the files the number of times that your administrator has configured.

Downloading Private Data

If you are downloading any private data, you are prompted to log in.

Once you log in, the NBIA Data Retriever appears.

If you do not have permission to access even one of the collections/sites to which the images you have in your manifest file, you are prompted to contact the help desk to request permission to access all of the images.


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Exporting Data to a Spreadsheet

Once data is in your cart, you can export it to a Comma-Delimited Values format spreadsheet for analysis or sharing with others.

To export your cart

  1. Add data to your cart.
  2. Click Cart button with 25GB label
    The cart appears.

  3. Click Export Spreadsheet button.
    A CSV file opens in your browser.
    The spreadsheet includes the following columns: Subject ID, Study UID, Study Description, Study Date, Series ID, Series Description, Number of images, File Size (Bytes), Collection Name, Modality, and Manufacturer.

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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 a 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.

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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, NBIA opens to the cart page. 

In the legacy NBIA data portal, this was called a shared list. 

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 a 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.

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