Dear folks (@ThomasBoudier),
I am running into memory issues with 3D Manager (Plugins > 3D > 3D Manager). I attempted analysis using a PC with 64 GB RAM available on it - the memory gets fully filled at some stage (it coped after ~2 hours with ‘3D Segmentation’, but not ‘Add Image’). The plugins seems to want to use more memory than it gets allocated by ImageJ (I increased the memory at Edit > Options > Memory & Threads to 65536 MB).
The dataset I have is 3728 x 3728 pixels x 48 slices (8-bit, 636 MB - this data was pre-processed and binarized). When downsized by half (1864 x 1864 x 24, 80 MB) 3D Manager copes fine; both ‘3D Segmentation’ and ‘Add Image’ complete within several seconds.
Has anyone ran into this memory challenge?
Dividing the original data stack into smaller stacks presents different issues with how to treat objects at the then newly created image edges. Ideally I will not do this. I am interested in the 3D orientation of objects in the image stack, I hoped to use the bounding box coordinates for determining this.
Possibly I should think about using Python or Matlab/Octave? Any possible recommendation here for 3D image processing?
Many thanks for any advice