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help > Vaa3D Out of Memory Error
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Apr 1, 2020 02:04 PM | jdp
Vaa3D Out of Memory Error
Hi
I am trying to load a 2.3 GB tiff stack file into Vaa3D and run the fast marching neuron swc generation algorithm. I am unable to load the tiff file with an out of memory error. I also tried to run the code from the command line and get the same out of memory error.
As this forum suggested, I tried loading the tiff stack file as a sequence of 2D images and I was able to load the images. Do you know how I can run the fast marching algorithm on a series of 2D images? The plugin gives a segfault when attempting to load it and running from the command line takes a stack as input. Is there something I can change in the code to allow for either a larger image or a 2D series of images?
Thanks in advance,
Jason
I am trying to load a 2.3 GB tiff stack file into Vaa3D and run the fast marching neuron swc generation algorithm. I am unable to load the tiff file with an out of memory error. I also tried to run the code from the command line and get the same out of memory error.
As this forum suggested, I tried loading the tiff stack file as a sequence of 2D images and I was able to load the images. Do you know how I can run the fast marching algorithm on a series of 2D images? The plugin gives a segfault when attempting to load it and running from the command line takes a stack as input. Is there something I can change in the code to allow for either a larger image or a 2D series of images?
Thanks in advance,
Jason
May 5, 2020 05:05 PM | Hanchuan Peng
RE: Vaa3D Out of Memory Error
2.3GB is not large, so there are
multiple ways to run tracing, if you have a computer with very
small amount of memory.
(a) try to run TReMAP.
(b) try to run UltraTracer.
(c) downsample your data and run APP2 directly.
(d) *** Important trick: you can indeed use the XYZ cutting planes in a 3D viewer to limit the range of tracing, in that way, you trace the full-resolution image, but for a smaller volume.
Originally posted by jdp:
(a) try to run TReMAP.
(b) try to run UltraTracer.
(c) downsample your data and run APP2 directly.
(d) *** Important trick: you can indeed use the XYZ cutting planes in a 3D viewer to limit the range of tracing, in that way, you trace the full-resolution image, but for a smaller volume.
Originally posted by jdp:
Hi
I am trying to load a 2.3 GB tiff stack file into Vaa3D and run the fast marching neuron swc generation algorithm. I am unable to load the tiff file with an out of memory error. I also tried to run the code from the command line and get the same out of memory error.
As this forum suggested, I tried loading the tiff stack file as a sequence of 2D images and I was able to load the images. Do you know how I can run the fast marching algorithm on a series of 2D images? The plugin gives a segfault when attempting to load it and running from the command line takes a stack as input. Is there something I can change in the code to allow for either a larger image or a 2D series of images?
Thanks in advance,
Jason
I am trying to load a 2.3 GB tiff stack file into Vaa3D and run the fast marching neuron swc generation algorithm. I am unable to load the tiff file with an out of memory error. I also tried to run the code from the command line and get the same out of memory error.
As this forum suggested, I tried loading the tiff stack file as a sequence of 2D images and I was able to load the images. Do you know how I can run the fast marching algorithm on a series of 2D images? The plugin gives a segfault when attempting to load it and running from the command line takes a stack as input. Is there something I can change in the code to allow for either a larger image or a 2D series of images?
Thanks in advance,
Jason