Even better would be something somewhat automated that can register the neuron of interest despite the significant displacement and deformation of the rest of the volume. I think I can do this with manual landmark selection in imagej, by selecting landmarks that are in or near my neuron of interest, but I haven’t found a plugin that makes it streamlined enough to be feasible for large datasets. About Press Copyright Contact us Creators Advertise Developers Terms Privacy Policy & Safety How YouTube works Test new features NFL Sunday Ticket Press Copyright. The plugin Landmark Correspondences does the job admirably well, however it seem to only preserve one channel of my images. I have multichannel images that I would like to align (center and rotate). ![]() In brief: for each pair of images that needs to be registered, the user has to choose the reference image and then select among 4 (optional) successive registration steps: rigid manual B.1affine auto B.2spline auto B.3 (based on landmarks)spline manual B.4. fiji, imagej, plugin, registration, channels. The embryo moves a lot, and changes as it grows, so I’m not sure if standard 3d image registration would work. The registration workflow, which happens within Fiji is described in Figures 2A,B. The full syntax follows one of the three cases below: -help. ![]() I would like to register the sequence so that I can visualize growth of the axon - ie have a specific neuron be in a fixed position while the rest of the image is rotated and translated to keep that neuron in position. Here is an example of a call to TurboReg from a macro: run ('TurboReg ', '-align -file path/source.tif 40 80 639 479 -file path/target.tif 0 0 639 479 -translation 320 240 331.7 210 -showOutput') A fully developed and commented example is available here. I have collected 4D image sequences of neuronal process growth in developing C. Hello - this is my first post so let me know if I’m not doing this right!
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