![]() ![]() The ending double hyphen "-" is to specify all of these are JVM arguments, not fiji/ImageJ arguments.This can cut the memory footprint by half in many cases. -XX:+UseCompressedOops : use 32-bit pointers when possible, in a 64-bit JVM.-XX:CMSTriggerRatio=50 : run the parallel garbage collector when the ratio of free versus non-free heap space is 50 % (the default is 92% in 64-bit JVM, which may incur in pauses and undesirable full sweeps).-XX:NewRatio=5 : Set the ratio of ephemeral versus more long-lived objects to 5 (the default is 9 or more in 64-bit Sun JVMs).-XX:PermSize=256m : preallocate the heap for the permanent objects directly to the desired maximum, 256 Mb, so it doesn't ever have to be resized.The default is only 32 Mb, which proves insufficient. -XX:MaxPermSize=256m : set the heap size allocated to objects that don't need to be garbage often to 256 Mb.not the super-new generation of allocated objects) using parallel threads. Clean up unused memory in the concurrent mark-sweep generation (i.e. -Xincgc : use the incremental garbage collector.Note it's the same amount as the intial heap size, so that the heap cannot be resized. -Xmx10g: use a maximum heap size of 10 Gb.start fiji with 10 Gb of RAM preallocated to it) -Xms10g : use an initial heap size of 10 Gb (i.e.XX:NewRatio=5 -XX:CMSTriggerRatio=50 -XX:+UseCompressedOops. ImageJ-linu圆4 -Xms10g -Xmx10g -Xincgc -XX:MaxPermSize=256m -XX:PermSize=256m ![]() The following configuration has been tested in a machine with 8 CPU cores and 16 Gb of RAM, running Ubuntu 8.04 "Hardy", with a 1.6.0_16 or newer JVM: Running fiji for heavy-duty, memory-intensive, high-performance TrakEM2 tasks TrakEM2 tutorials with video tutorials.xml file onto the toolbar, or via "File - Open". Open an existing project by dragging its.Create new projects from "File - New - TrakEM2 (blank)".TrakEM2 interacts with the 3D Viewer for visualization of image volumes and 3D meshes. Semantic segmentation: order segmentations in tree hierarchies, whose template is exportable for reuse in other, comparable projects.Image Annotation: floating text labels.3D Visualization: interacting with the 3D Viewer plugin, TrakEM2 displays image volumes and 3D meshes of all kinds.Image Registration: register floating image tiles to each other using SIFT and global optimization algorithms.Measurements: volumes, surfaces, lengths, and also measurements via ImageJ ROIs.Skeletonize entire neuronal arborizations and represent synapses with relational connector objects. Segmentation: manually draw areas across stacks, and sketch structures with balls and pipes.6 How much RAM should I allocate to the JVM for Fiji to run TrakEM2?.5.4 Faster XML loading and less memory consumption with larger quadtree buckets.5.3 For regenerating mipmaps the fastest possible.5.2 For importing large collections of images and editing them immediately afterwards.5.1 For fastest browsing through layers.5 Preparing TrakEM2 for best performance.4 Running fiji for heavy-duty, memory-intensive, high-performance TrakEM2 tasks. ![]()
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