![]() ![]() This is maybe a far stretch but is there an easy way to e.g. ![]() ![]() Unfortunately, that means I can’t use it on my data specifically. However, the algorithm behind your Shift function isn’t quite as precise as the one that’s running the ‘template matching’ plugin. the ‘Template matching’ plugin is unable to do that, since it only works on single channel stacks. If journal reference limits interfere, the plugin-specific publications should. If you used the original ImageJ, cite the ImageJ paper. If you used ImageJ2, cite the ImageJ2 paper. The general paper of ImageJ flavor (s) used e.g.: If you used Fiji, cite the Fiji paper. I couldn’t find any information on that in the documentation, code or in Google. We ask users to cite: Any specific publications of plugins used. Hello, I was wandering which type of interpolation is used when re-slicing an image with the re-slice function in Fiji (Image->Stacks->Reslice). StackReg takes a stack with misaligned slices and aligns the slices with respect to the current slice. channel 1 as a template, and it will apply those values to alle channels in the hyperstack. Interpolation type of 'Reslice' function in Fiji. The plugins StackReg (to align a stack) and TurboReg (to align more than one image or stack) can be used for alignment and are found at 'Plugins/Registration/StackReg or TurboReg'. ![]() A stack with 20 slices would be converted to 20 normal image windows. Being able to use the Shift function that is part of your plugin would simply solve everything, since you can use e.g. Stack to Windows Converts the currently active stack to windows.Channel 1 (phase contrast) is used as reference. Older versions: Description: Repairs displacement of fluorescence channels in bacterial images. Is there any way that you can comment on how this can be solved? : Version 16 (works with ImageJ 1.50d) : Version 15 : Version 14 : First version: Source: AlignFluorChannels17.txt A demo stack is available. More specifically, when I right click on the table I immediatelly get the following error message:Įxception in thread “AWT-EventQueue-0” I wanted to try the newer Multi-Template Matching plugin for this same purpose. I am unable to copy paste the ‘shifted value data’ originating from the ‘template matching’ plugin into the CoordinateShift table. Hi, I have been using Template Matching plugin to align timelapse images loaded as stacks in FIJI.There are however two things that are still preventing me from solving my issue: I’ve tried your plugin and it has some fantastically usefull features. Thanks.It’s been a while, but I’m picking up this topic once again. Poorman3DReg, looks like an old plugin and when I tried it it wouldn’t work on my computer, but theoretically this does what I’ve described with StackReg + apply to each z level.Īny input for existing solutions that would work better (or faster!) than this would be appreciated. I think this will do what I want as it’s essentially stackreg that saves out the transform, so I could write a macro that uses MultiStackReg on the z-projection to get the transform, then makes substacks at each z-slice of the original z-stack, applies the transform to each one, then re-stacks the slices. Template Matching and Slice Alignment It is highly recommended to install this plugin us) built-in update manager (ImageJ's Menu>Help>Update.), and add the following URL via 'Manage update. I may have included too many of the edge z-slices. correct_3d_drift plugin, which I think theoretically does what I want, though the results on my stack weren’t great for xy drift correction. Note that I don’t need something to align slices in z at one time point essentially what I want is to apply StackReg of the z-projection to each z-level of the stack across time (or some better computational method).Some things I’ve come across so far include: Doing stackreg on each z-slice independently probably isn’t a great idea as there won’t be much structural information to use toward the edges of the stack. For example, I have a 13 z-step by 30 timepoint z-stack, where I want to correct for drift across time in all slices. In this case however, I want to have all slices of the stack registered across time (the image is eventually going to Imaris, which uses the z-stack information). Normally, I use StackReg on a z-projection and that works great. I am looking for a plugin or solution to align a z-stack of images across time. ![]()
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