Stitching & Deconvolution Wizard

The Huygens Stitching & Deconvolution wizard is GPU accelerated, and offers a unique easy-to-use option for combined high-quality stitching for all types of microscopy data with the additional option to deconvolve the images, and to correct for vignetting issues. Vignetting correction can be performed manually and in a full automated fashion. The Stitching & Deconvolution Wizard is available for Huygens Essential and Huygens Professional. All file types supported in Huygens can be stitched (some by providing an XML file with layout/location information). The layout information from DeltaVision, LIF, and CZI formats is loaded automatically. Additionally, the tool offers controls to adapt the acquisition pattern for when the meta data is not accurate enough.

Please note that this Stitching & Deconvolution Wizard works with tiles and is a different tool than the Fusion & Deconvolution Wizard, which is specifically built for fusing multi-view Lightsheet and SPIM images.

Automatic Vignetting correction and Stitching

No Vignetting Correction
Auto Vignetting correction

Huygens stitched tiles of widefield (Leica) fluorescent Leica LIF data. The same data is shown with and without Huygens automatic vignetting and shading correction. Image represents a developing mouse cortex (P30) stained for Tbr1 and reelin. Courtesy of Dr. Kolk and Dr. Witteveen (Nijmegen Centre for Molecular Life Science, The Netherlands)

Stitching of a Zeiss CZI with more than 1,700 tiles

An impressive 1700+ tile compound merged by the Huygens Stitcher to a large 60GB dataset. Notice the scaling bar indicating 2 mm. Raw data by © Carl Zeiss Microscopy GmbH.


  • Mosaic preview of the tile content.
  • Optimal positioning of each tile to guarantee smooth transitions across regions of overlap.
  • Tiles with 0% overlap can still be stitched.
  • Registration and deconvolution is supported by GPU .
  • Support for 2D, 3D, multichannel, and time series images.
  • 3D position optimization in X, Y and Z.
  • No limit to the number of tiles that can be stitched.
  • No limit to the total file size of the input sequence.
  • Stitches all file types supported in Huygens (some by providing an XML file with layout/location information).
  • Reads layout information from DeltaVision, LIF, CZI formats automatically
  • Improved support for custom stitching patterns.
  • Automatic vignetting estimation and correction for each channel.
  • Manual vignetting and shading correction option by including recorded flat-field and dark-frame images.
  • Choice for only stitching and optional vignetting also possible by simply skipping deconvolution in this wizard.
  • Integrated Huygens deconvolution for the merging of restored tiles.

The Stitching & Deconvolution wizard at work

The Stitching & Decon Wizard can be started in Huygens Essential and Professional via the Deconvolution menu. If Nikon ND2 (Windows only), Leica LIF or Zeiss CZI images containing layout information are opened, the tile content will be automatically recognized and opened in the Stitcher Wizard. All other file types supported in Huygens can be stitched by providing a XML file with layout information.

Upon file opening, the wizard user interface will show the tile order. If needed, the acquisition pattern, start, percentage of overlap, and number of rows can be adjusted. Tile content can be previewed, and tiles can be selected/unselected for stitching. Automated and manual correction options are present to address any possible vignetting and shading issues. When all set, the Huygens stitcher will correct the tiles for shading effects and optimize the tile layout by analyzing the overlapping regions.

The Huygens Stitching & Decon wizard offers the unique possibility to automatically deconvolve each tile before the actual stitching is applied. For this purpose, a Parameter and Deconvolution template can be simply loaded within the wizard. By combining deconvolution, stitching, and shading correction in one single workflow, the Huygens Stitcher is able to make optimal use of hardware resources that are available.

For more information on the use of the Huygens Stitcher, we like to refer you to the Essential and Professional Manuals and to the Huygens Stitcher Tutorial Video.

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Contact Information

Scientific Volume Imaging B.V.

Laapersveld 63
1213 VB Hilversum
The Netherlands

Phone: +31 (0)35 64216 26
Fax: +31 (0)35 683 7971
E-mail: info at svi.nl

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