![]() ![]() Compute the boundary contours (Panel 2: Compute boundary contours).A message will be displayed in the script editor output panel informing of the selected RoiSet. This will open the image stack and it will load the ROIset file that is expected to be saved in the same directory. (These can be set by the user if more than two contours are defined on each slice in step A.3.2).Ĭlick "Load scanStack", navigate to the directory of your image stack, select one image and click "Open". Select the inner and outer contour ID as 0 and 1 respectively. Select the "contour definition" as "Load ROIset" The "sample type" will be stored in the auto-generated log file for future reference. "Sample type" holds a user-given identifier of the sample and it is irrelevant to any computation. Begin by setting this equal to the number of slices in-between the defined contours (though it is not necessary that these two values are the same.) Depending on how "quickly" the deformed tube changes from slice to slice this number will vary. interpolation to create missing contours in-between slices. The interpolation interval corresponds to the vertical axis i.e. If a sub-stack is to be unrolled, set the "First slice" and the "Number of slices" accordingly. If the deformed tube extends over the entire image stack, set the "First silce" to 1 and the "Number of slices" to 0. This is helpful if a working set of parameters is saved using the "Save parameter file" button in Panel 3. "Custom" : A cyclorama parameters file assumed to be located in the directory of the image stack. plugins/3Dcyclorama/defaultCycloramaParameters.txt. ![]() "Default" : A predefined set of parameters that is located at. "Previous" : Parameters saved during the last exit of the 3D cyclorama plugin. The 3D cyclorama plugin should appear in the Plugins menu towards the bottom in a menu titled 3D cyclorama.Extract the contents of FastDTW-master (FastDTW.iml, README.md, src, target, etc.) in Fiji.app/plugins/FastDTW.Download the FastDTW algorithm from github (Click code > download zip).Create a directory named FastDTW in the Fiji plugins directory (Fiji.app/plugins/FastDTW).Go to Help > Update > Manage update sites.“3D cyclorama for digital unrolling and visualisation of deformed tubes.” Sci Rep 11, 14672 (2021). If you use this plugin for your research or industrial applications we kindly ask you to cite our work. If you’d like to help, check out the how to help guide!įiji plugin to digitally unroll deformed tubes. The content of this page has not been vetted since shifting away from MediaWiki.
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