help > Vaa3D Out of Memory Error
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Apr 1, 2020  07:04 AM | 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
May 5, 2020  10:05 AM | 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:
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