2017-07 MAN-C0034-06
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NanoString Technologies
®
USER MANUAL
Report Integration with External Systems
The nCounter Dx Analysis System supports direct integration with existing report generation and management systems, such as Laboratory
Information Systems (LIS). Using SFTP for file transfers, external automated processes may retrieve the output report (either in whole or in
part), as well as the system backup archive.
The retrieved reports are in formats suitable for integration with existing processes and systems. For downstream integration, the system
makes the report available as a PDF file identical to that which can be downloaded through the web GUI, as a PDF of the NanoString default
report (if different from the current report), and as a modular set of graphic files which can be incorporated into downstream system output.
System Access
For LIS integration, the
SSH Server
must be enabled (see
System Settings
). The username and password specified in
SSH Settings
for the
assay can be used with any file transfer tool which supports SFTP (SSH File Transfer Protocol). This protocol is widely supported by such
tools as WinSCP and PuTTY PSFTP on Windows and Transmit on Mac OS X. Access to the SSH Server is read-only: no files may be modified,
uploaded, or moved.
Assay-specific files:
After gaining access to the SSH server, the assay-specific files are arranged as follows:
Assay directory
Description and contents
/(login directory)
Top-level directory, contains XML export files and all subdirectories listed below
PDF files. For each completed sample, the NanoString standard report will always be present; if a
customized report has been defined, the PDF of that report will also be in this directory.
/image
Organizing directory for modular images.
/image/<basename>
One directory for each sample, named as described below. Each directory contains a series of images
which compose the full assay report and an HTML file to assemble the images in the original order. See
below for details.
/deprecated
All files which have been deprecated by using the
Edit an Analyzed Sample
function to generate a re-run
of the report algorithm or other update. These are the original, unchanged files.
Modular Images
The /image/<basename> directories contain a series of high-resolution (300 dpi+) images which may be used by advanced organizations.
Header, footer, and signature images may be modified to include organization-specific information, or may be completely replaced by
organization-provided equivalents, or may be omitted entirely. Body images may not be modified and should be used complete and as-is
only.
The supplied HTML file serves as an “inventory” and may be used to ensure that downstream systems have retrieved body images and/or
headers and footers for every page of the report. It can serve as a template for further modifications.
