![]() Shrinkage constrain, in other registration models, this guaranties a non-shrinking registration.Advanced setup, to specify the feature extraction parameters.The feature extraction and registration models: in this case, and as mentioned before, we only need a translation to model the transformation.Īnd we click on the first two check-boxes:.The output directory: we set it to the folder where we want to store the final aligned slices.The source directory: we set it to the stitching output folder so the plugins will align the stitched images.Alignmentįor the alignment of the stitched slices we will use the plugin Register Virtual Stack Slices, under Plugins › Registration:Īs before, a dialog will pop up where we have to choose the registration parameters: Performance: The stitching of the 19,600 images (732x732 pixels each) took around 117 minutes in a Intel Core Duo at 3GHz, 4GB of RAM, running on Linux 64-bit. The plugin will display all intermediate results until the whole sequence has been stitched.Īfter processing the last grid/section, the plugin will display the following message:Īs result, the stitched images are stored in the output folder: We then click on OK and the stitching will take place. The default value (0.3) is quite low, but in our test case works perfect. The regression threshold: the number below with the plugin won’t accept correlation values as valid. ![]() In our test case we won’t fusion the images, so we select None. The fusion method: the way the plugin will treat the overlapping areas.The output directory: the folder to store the resulting stitched images.All the images are stored in the same folder and have an intuitive sequencing name (such as Tile_X(xxx)_Y.png.The transformation between slices can also be modeled as pure translation. Given the origin of the images used in this tutorial, the transformation between tiles can be modeled as a pure translation to generate the mosaic (of a slice). This tutorial describes ’ how to produce an image stack (or 3D image) from an input sequence of tiles’ using the Fiji plugins for stitching and registration. If you’d like to help, check out the how to help guide! Introduction The content of this page has not been vetted since shifting away from MediaWiki.
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