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Stitcher Wizard


The Huygens Stitcher wizard, available for Huygens Essential and Huygens Professional, offers a unique easy-to-use option for combined high-quality stitching with deconvolution, and automated or manual vignetting correction.

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.


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.



Features

  • 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.
  • 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 information).
  • Reads layout information from LIF and 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.
  • Integrated Huygens deconvolution for the merging of restored tiles.

The Stitcher wizard


The Stitcher can be started in Huygens Essential or Professional via the Deconvolution menu. If 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 file types supported in Huygens can be stitched by providing an extra XML file with layout information.

Once the tiles are loaded it is possible to check the order of the images. This can be defined by the meta data or adjusted by the user. For the loaded tiles the acquisition pattern, start, percentage of overlap and number of rows can be selected. You can help yourself in this stage by previewing the tile content by selecting “Show tile contents”, and eventually select the tiles you want to include. After the adjustment and the selection of the tiles, it is possible to proceed with vignetting and shading correction. The stitcher will correct the tiles for shading effects and will optimize the layout by analyzing their overlapping regions.

Furthermore, the Huygens stitcher wizard offers the unique possibility to deconvolve each tile with Huygens deconvolution before stitching. By doing so, Huygens does not only facilitate the workflow, but also optimizes the resources that are needed for deconvolution and stitching. In order to deconvolve the tiles before stitching, the Parameters template and the deconvolution template have to be loaded. At the end of the process it is possible to export the results or restart the wizard to use other settings.