Stitching


Welcome to this tutorial on the Stitcher
in Huygens. This option is available for Huygens essential and professional. The Stitcher offers a unique solution for combining high quality stitching with deconvolution. This integrated approach offers the advantage of minimizing the resources needed for obtaining restored contrast-rich and high-resolution images of large objects. Furthermore, the post-acquisition
workflow is considerably simplified for the user. The Stitcher Wizard can be
started in Huygens from the deconvolution menu. If Leica LIF or Zeiss CZI images with tiles or a XML file with accompanying tiff tiles are opened the tile content will be automatically recognized and opened in the stitcher wizard . If this is not the case you can manually select the tiles through the Stitcher wizard. Here you see the stitcher wizard. Press
load multitile images to proceed. Here you see our example image selected. It has 24 tiles We will select them all and proceed with the Stitcher. Once they have all been selected, we press accept and the Stitcher will preview the shape. If the position of the tiles is known from metadata, the Stitcher wizard will continue with tile selection. However, if the ordering of the tiles is
not specified within the metadata a Stitcher window will be presented with
options to customize the stitching pattern. For the loaded fileserie, you can select the acquisition pattern as shown here. You can select the acquisition
pattern, the acquisition start, the acquisition overlap and the number of
rows. In order to help yourself in the selection, you can preview the content of your files by pressing the show tile contents button. We used a CZI file however, so the pattern was automatically acquired by the metadata . In this window
you can specify which tiles you want to select. Again, you can facilitate the
selection by showing the content of the tiles by pressing show tile contents. Press the arrow to continue. The tiles of a Stitched mosaic often
suffer from vignetting and shading because of uneven field of illumination. To correct for these artifacts, the Huygens Stitcher is equipped with an automatic
vignetting/shading correction. As an alternative, there is a manual vignetting and shading
correction option which flat-field and dark frame images need to be loaded. We will however use the automatic mode here. Here you can choose which channels will
be corrected for vignetting and if you want to use the default, circular or
ellipsoidal model for the vignetting. The severity of the vignetting can be
adjusted with the slider. As displayed, you can now choose which
channels you want to use in the optimization process. In the optimization
stage, the wizard will calculate the optimal transitions between pairs of
tiles for the minimization of tiling effects. Furthermore, the Stitcher wizard
offers the user the unique possibility to deconvolve each tile automatically
before stitching. By doing so, Huygens not only simplifies the workflow
but also minimizes the processing workload that would be needed for deconvolving a stitched mosaic image. To deconvolve the tiles before stitching,
you just need to select the microscopic template and deconvolution template. These templates should be created or edited first, before starting the Stitcher
wizard by using the options at the deconvolution stage that you can see here. Now you can start stitching the tiles. Here you can see the stitched image. You can export
the result by pressing done or restart the stitching if you want to change the
settings of the stitching. if you select quit, the result will not be exported. Thank you for watching, if you have any
questions feel free to contact us.