8/16/2023 0 Comments Imagej particle analysis![]() For large images (512 x 512 x 512) and above, use 2, for smaller images, 3 or 4 may be faster on your system. Slices per chunk: number of image slices per thread when using the Multithreaded particle-labelling algorithm.Fast on big stacks, but only if you have the memory. ![]() Linear: Non-recursive but heavy on RAM and single-threaded.Fast on small stacks and if you have many CPU cores. Multithreaded: use multiple cores and job chunking to reduce recursion.Mapped: Non-recursive and memory-efficient, fastest method but with slightly higher memory requirement than Multithreaded.Volume resampling: amount of voxel resampling to apply when displaying the original stack.Split value: Particles with volume greater than this value are coloured red, otherwise coloured yellow.Split: Each particle is coloured depending on whether it is over (red) or under (yellow) the Split value.Gradient: Each particle gets a unique colour between red and green.Show stack (3D): display the original binary stack in a 3D Viewer window.Show axes (3D): display principal axes (from moments of inertia) in a 3D Viewer window.Show surfaces (3D): display particles' surface meshes in a 3D Viewer window.Show size stack: display an image with particles labelled by their volume.Show ellipsoids (3D): display best-fit ellipsoids in a 3D Viewer window.Show centroids (3D): display particles' centroids in a 3D Viewer window.Show thickness stack: display the result of local thickness in a new stack.Show particle stack: display an image containing labelled particles.The effect of this option can be visualised with Isosurface. Surface resampling: how much to resample the stack while creating the surface mesh by marching cubes.Max Volume: largest particle to measure or display.Min Volume: smallest particle to measure or display.Record unit vectors: log the unit vectors of the inertia tensor and best-fit ellipsoid's axes to the Results table.Ellipsoids: find the best-fit ellipsoid to the particle's surface mesh.Euler characteristic: measure each particle's Euler characteristic and connectivity. ![]()
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