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Discovery Control Panel User Guide

Introduction

Discovery is built on open source XNAT. It allows you to:

  • configure connections between PACS or VNA
  • index the DICOM metadata
  • manage data requests that come from Discovery Dashboard
  • create data requests from a list 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 to index a PACS or VNA and create data requests, as well as monitor both indexing and requests.

Instruction Steps

Indexing the PACS into Discovery

In order to get a cohort-centric view of DICOM metadata in Discovery Dashboard, PACS must be indexed. 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. (Note: more than one indexing job can run simultaneously, which will often increase throughput)

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:

  1. Navigate to Site Administration in the top navigation menu and select Discovery Control Panel.
  2. Select the Indexing tab, and then select New Index Job.
  3. Choose the date range to index, select the Update Existing Records checkbox to update existing metadata.
  4. Select Begin Index. The time required for indexing will vary depending on the PACS system, network connectivity, and the number of studies that require indexing.

execute index

Viewing and Canceling Indexing Jobs

Indexing jobs can be monitored including job status and how many days are complete out of days requested.

To view, cancel, or restart indexing jobs:

  1. Navigate to Site Administration in the top navigation menu and select Discovery Control Panel.
  2. Select the Indexing tab.
  3. Depending on the job state, the indexing job can be canceled or restarted.

view index

Viewing Indexing Status

Indexing progress can also be viewed based on DICOM Study Date. This can provide a general idea of what has been indexed and what is missing.

  1. Navigate to Site Administration in the top navigation menu and select Discovery Control Panel
  2. Select the Indexing tab
  3. At the bottom, a histogram displays a daily count of DICOM study dates that have been indexed. As indexing occurs, this histogram will be populated.
  4. The histogram can be viewed based on a preselected or custom date range, which can be selected from the View date range dropdown or by clicking and dragging on the historgram.

Data Requests

A data request is a collection of Study Instances or Accession Numbers that identifies a cohort of interest. Once a request is fulfilled, further analysis can be performed.

There are currently two methods to submit a data request to Discovery Control Panel:

To manage Data Requests, please follow the below steps:

  1. Navigate to Site Administration in the top navigation menu and select Discovery Control Panel.
  2. Select the Data Requests tab.
  3. Select a row in the Data Requests table to see more information about that request, including the requesting user, associated IRB number, number of studies requested, Discovery query details and the requested study identifiers.

view request

Discovery Dashboard

  1. From the Discovery Dashboard, once you have filtered to the desired cohort, select the Request Cohort button. This will send the list of filtered studies to the Discovery Control Panel data request service.
  2. The request will remain in PENDING state until a site admin selects the Approve on the data request. More detailed information on dashboard filtering is available in the Discovery Dashboard Documentation.

dashboard request

Upload a CSV File

  1. To submit a Data Request, upload a CSV file containing either Accession Numbers or Study Instance UIDs with the appropriate header, see supported formats below.
  2. Choose New Request from the Data Requests screen
  3. Once the request has been submitted, it will appear in the Data Requests table in the Control Panel.

submit request

The CSV upload 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

Approving a Data Request

A data request will be in PENDING state until an admin approves the request.

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

  1. Select the desired data request from the table.
  2. Select Approve Request which gives the option to link to a cohort project.
  3. Select a project to link to or Download Only and select Aprove Request again to begin downloading.

Studies are only downloaded once from the source PACS and saved in an archive project. If a Link Request project is selected, the images will be available in this project upon completion.

approve request

Monitoring a Data Request

Select a data request from the table to get more details.

request status

  • PRE_PROCESSING - Study identifiers are being resolved on PACS
  • PENDING - Request has been saved to the database and awaiting approval
  • DENIED - Data request has been canceled
  • PROCESSING - Request has been approved, queud for downloading
  • DOWNLOADING - Imaging data downloading from PACS
  • COMPLETE - All studies downloaded successfully
  • COMPLETE_WITH_ERRORS - Finished processing, some studies in error state
  • ERROR - Unexpected issue, admin is notified and request can be retried
  • FAILED - Admin is notified and the request cannot be retried

Request Study Statuses

Each study has its own status with more details.

request status

  • REQUESTED: study has been requested as part of the data request
  • QUEUED: study has been queued for retrieval from PACS
  • DOWNLOADING: at least one instance from the study has been received from PACS
  • DOWNLOADED: all instances from the study have been received from PACS
  • AVAILABLE: study is available for use in the data request project
  • ERROR: there was an issue during any step in the process. See the status message for details.

Data Request Linked Cohort 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 Core using the Flywheel Integration container.

Screenshot_2023-01-17_at_8.08.53_AM.png

Resources

Discovery Dashboard Quick Start

Discovery to Enterprise Data Export

Discovery Control Panel Configuration