Discovery Admin User Guide

1. Introduction

Discovery Admin is built on open source XNAT and provides the ability to configure connections between Picture Archiving and Communication System (PACS) or Vendor Neutral Archive (VNA), index the Digital Imaging and Communications in Medicine (DICOM) metadata, which will expose a high level view of the imaging data. Discovery Admin also enables management of data requests that come from Discovery Dashboard and allows uploading of imaging study identifiers. Data requests can then be pulled as full imaging studies from your clinical imaging system and staged for further processing and analysis. 

This document provides instructions on how to index your PACS and create data requests, as well as monitor both indexing and requests. 

1.1 Indexing the PACS into Discovery

In order to get a cohort-centric view of DICOM metadata in Discovery Dashboard, it is necessary to index PACS. This is the first step in populating the data that will be used in your visualizations. Once the Discovery plugin has been configured and the appropriate PACS and Service Class Provider (SCP) receivers are in place, Discovery indexing can be executed.

2. Instruction Steps

2.1 Executing an Indexing Job

Indexing jobs are handled on a per date basis that correspond to the DICOM StudyDate tag. Execute for all days desired to visualize and build imaging cohorts from your PACS.

To execute an index job, go to under Site Administration in the top navigation menu:

1. Select Discovery Control Panel
2. Select the Indexing tab
3. At the bottom of the page, choose the date range to index (note: the Request Start Date must precede or be the same as the Request End Date)
4. To update the existing metadata when launching an indexing job, turn on the Update Records button
5. Select Request Indexing. The time taken for indexing will be very dependent on the PACS system accessed, network connectivity and the daily number of studies that require indexing
6. Selecting the blue refresh button at the bottom-left of this tab will update both the Requests and the Daily Counts tables

 

2.2 Viewing and Canceling Indexing Jobs

Indexing jobs can be monitored on a per job basis. This will display how many days are complete out of days requested.

To view or cancel indexing jobs, under Site Administration in the top navigation menu:

1. Select Discovery Control Panel
2. Select Indexing

Previous and running indexing jobs can be reviewed and canceled on this screen. Also, daily progress per job will be displayed.

 

 

2.3 Viewing the Daily Indexing Status

Indexing progress can also be viewed based on DICOM Study Date. This provides a general idea of what has been indexed and what is missing. Under Site Administration in the top navigation menu:

1. Select Discovery Control Panel
2. Select Indexing

On the right side of the page, a summary of the indexing status based on a daily count is displayed. As indexing occurs, this table will be populated.

 

2.4 Data Requests

A data request is simply a collection of Study Instances or Accession Numbers that identifies a cohort of interest. There are currently two (2) methods to submit a data request to Discovery Admin, (1) as a Comma-Separated Values (CSV) upload, or (2) as a submission from the Discovery Dashboard. Once a request is fulfilled, further analysis can be performed.

To manage Data Requests, please follow the below steps:

1. Under Site Administration in the top navigation menu, go to the Discovery Control Panel
2. Select Data Requests

More information about the request can be viewed when selecting rows in the Data Requests table including the requesting user, comment, date, Discovery query details and the requested UIDs.

 

2.5 Submit a Data Request: Option 1 – Upload CSV File

1. To submit a Data Request, begin by using the file downloaded from the Discovery dashboard or other available clinical systems
2. Then choose New Request from the Data Requests screen

Once a request has been submitted it will be placed in a DICOM Query Retrieve queue and imported using the same mechanism used by the DQR Plugin. 

 

 

The CSV upload currently supports the following formats:

Study Instance UID
1.2.3.876.3456544.224455.9989
1.3.2.876.3456544.224455.1233

Accession Number
12345678
98765432

 

2.6 Submit a Data Request: Option 2 – Discovery Dashboard Button

From the Discovery Dashboard, a user can select the Request Cohort button on the Study Instance UID visualization. This will send the list of filtered UIDs to the Discovery Plugin data request service. The request will remain in PENDING state until a site admin selects the Download action from the table. More detailed information on filtering is available in the Discovery Dashboard Documentation.

 

2.7 Approving a Data Request

A data request will be in PENDING state until an admin approves the request. To start the process, see the steps below:

1. Select the desired data request from the table
2. Select a project to link to
3. Then select Approve to start the process

Prior to linking a data request, one will need to create a new project for this data request if it does not already exist. To create a project, go to New -> Project in the top navigation menu.

Note: If you're sending the images to Flywheel Enterprise, use the project ID that you want displayed in Enterprise.

Once the request is passed to the DQR plugin, the status should change to SUBMITTED.

 

 

2.8 Monitoring a Data Request

The DQR Plugin gives one the ability to view a history of previously requested sessions, as well as a view of current requests that have been queued for import. This is available at Discovery Control Panel > Ingestion > PACS Requests.

 

I

 

2.9 PACS Requests Status Codes

The status field for items in the DQR Import Queue and Import History can be any of the following:

• QUEUED – request is in the Import Queue and has not been submitted to PACS
  
• PROCESSING – request is being processed for submission to the PACS (this is typically a very ephemeral status)
  
• ISSUED – request has been issued to the PACS and XNAT is waiting for a response
  
• FAILED – request has been denied by the PACS, or the PACS was offline and could not accept the request 
  
• RECEIVED – request has been approved by the PACS and data has been received

2.10 Viewing Archive Status

Once the download requests are picked up by the PACS, the imaging sessions should start to appear in the Archiving Activity section. Of special note, entries in this table will disappear as the data is moved into the master date based projects; the table will empty assuming all imaging sessions are archived successfully. If there are any errors, the entries will remain in the table in ERROR state.

• RECEIVING – DICOM data is incoming from PACS
• _BUILDING – Imaging session is being built in cache space
• _ARCHIVING – Imaging session is being moved to the archive
• ERROR – Something happened with the archival process. One can hover over the error to read more details.

 

 

Sessions will start to appear in the Recently Processed section on the Discovery Control Panel.

 

 

2.11 Data Request Linked Project

This project provides a view into the cohort requested by the researcher. Data can be analyzed and processed further in this project or it can be sent to Flywheel Enterprise using the Flywheel Integration tool.

A linked project now exists for the data request which will behave just like a normal XNAT project from the user’s perspective.

 

 

3. Resources