Plugin: Register Image - NIES-EPFL Transform for Aligning GCxGC and GCxGC-MS Data

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Joined: June 12th, 2013, 10:43 am

Plugin: Register Image - NIES-EPFL Transform for Aligning GCxGC and GCxGC-MS Data

Post by cheble » March 6th, 2018, 6:42 pm

The NIES-EPFL Transform plugin implements the alignment methods based on:
  • Algorithm A: Gros, J., Nabi, D., Dimitriou-Christidis, P., Rutler, R., Arey, J. S., “Robust algorithm for aligning two-dimensional chromatograms”, Anal. Chem. 2012, vol 84, p 9033-9040.
  • Algorithm B: Zushi, Y., Gros, J., Tao, Q., Reichenbach, S. E., Hashimoto, S., Arey, J. S., “Pixel-by-pixel correction of retention time shifts in chromatograms from comprehensive two-dimensional gas chromatography coupled to high resolution time-of-flight mass spectrometry”, Journal of Chromatography A 2017, vol 28, p 121-129.
The plugin allows GC Image users to use these two alignment methods directly through the Register Image action. Also, the original Matlab implementations are available at


The NIES-EPFL Transform plugin requires Version 2.6 or later.
  1. Download here: the NIES-EPFL Transform plugin
  2. Unzip it using File Explorer or another application.
  3. Start GC Image.
  4. From the menu, select Tools > Manage Plugins...
  5. Click on Import and then select the NIES-Alignment.plugin folder.
  6. Press OK to finish the installation. NIES-EPFL Transform will now be listed in the table.

To align chromatograms using NIES-EPFL Transform, select Processing > Register Image... in Image or Run > Register Images in Project. The NIES-EPFL Transform option will become available in the Transform Type combo-box. More details related to the Register Image action can be found in the User Guide.

The plugin can be configured to perform either of the two original methods as follows:
  1. Algorithm A for non-MS data
    • Choose to use Bicubic as the Interpolation Type.
  2. Algorithm B for MS and HRMS data
    • For HRMS data, choose to use Nearest Neighbor as the Interpolation Type.
    • For MS data, from Configure > Settings > Multi-Channel select By Integer Intervals for the MS Data Binning, and choose to use Bilinear as the Interpolation Type.
There are two additional configuration settings provided for Algorithm A and B. These settings can be modified through the menu Tools > Manage Plugins... Select the plugin from the table and click on the Configure button on the tool bar.
  • Typical peak widths (Col I and Col II) in pixel units, which defaults to 3 and 120 pixels.
  • The deformation correction enabled flag in true or false, which defaults to true.
Note: In addition to Algorithm A and B, the software supports HRMS data for all interpolation types by using the GC Image's MS Data Binning settings.

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