Hello,

I was wondering if there is a way to run app2 from command line that will execute neuron tracing on a directory of 2d tif images, that when stacked together will construct the 3d neuron of interest. The script will not run if a .tif image is not given in the /i parameter. (Windows 10 user, Vaa3d v3.475)

Alternatively, is there a command line functionality in Vaa3d that creates an image stack from an image series?

Thank you,

Matt

Yes, you can import a series of image sections and save as a 3D tiff stack. Check the 'import' function in main menu.

No, we do not support running APP2 for the 2D folder. The code is there, you may write a wrapper to load data first followed by APP2 tracing.


Originally posted by Matt Mallory:

Hello,

Thank you for the detailed response. I am trying to use Fiji to convert my 2D folder of tif images into a .v3draw file so that there are no tiff formatting issues when loading into vaa3d. In Fiji I load the image directory as a virtual stack and then just export as .v3draw file.
However, when I use this v3draw file with vaa3d app2, I am now getting an error as shown below.

I was wondering how can I fix this issue?

The current input file has the suffix [v3draw]
The data does not have supported image file suffix, -- now this program assumes it is Vaa3D's RAW format and tries to load it...

size of [V3DLONG]=[8], [V3DLONG]=[8] [int]=[4], [short int]=[2], [double]=[8], [float]=[4]
The data endian code is
The machine endian code is [L]
machine endian=[L] data endian=[b] b_swap=1
mysz raw read unit[0]: [-2145583104] swap unit: [7552][1d80]
mysz raw read unit[1]: [-2145583104] swap unit: [7552][1d80]
mysz raw read unit[2]: [1023541248] swap unit: [573][23d]
mysz raw read unit[3]: [16777216] swap unit: [1][1]
Fail to allocate memory in loadRaw2Stack().
The data doesn't look like a correct 4-byte-size Vaa3D's RAW file. Try 2-byte-raw.
The size of your input file is too small and is not correct, -- it is too small to contain the legal header.
Error happens in reading 4-byte-size and 2-byte-size Vaa3D's RAW file. Stop.[/b]

Actually was able to load the image, however when trying to run app2 it fails as seen below. I get a memory error with My4DImageSimple, and the v3draw image is only 31GB. I have the 128Gb iunstalled RAM. What memory is this error referencing?



Just read 2147483646 units, each unit has the size = 1
Finish reading 6.5713%
Just read 2147483646 units, each unit has the size = 1
Finish reading 13.1426%
Just read 2147483646 units, each unit has the size = 1
Finish reading 19.7139%
Just read 2147483646 units, each unit has the size = 1
Finish reading 26.2852%
Just read 2147483646 units, each unit has the size = 1
Finish reading 32.8565%
Just read 2147483646 units, each unit has the size = 1
Finish reading 39.4278%
Just read 2147483646 units, each unit has the size = 1
Finish reading 45.9991%
Just read 2147483646 units, each unit has the size = 1
Finish reading 52.5704%
Just read 2147483646 units, each unit has the size = 1
Finish reading 59.1417%
Just read 2147483646 units, each unit has the size = 1
Finish reading 65.7130%
Just read 2147483646 units, each unit has the size = 1
Finish reading 72.2843%
Just read 2147483646 units, each unit has the size = 1
Finish reading 78.8556%
Just read 2147483646 units, each unit has the size = 1
Finish reading 85.4269%
Just read 2147483646 units, each unit has the size = 1
Finish reading 91.9982%
Just read 2147483646 units, each unit has the size = 1
Finish reading 98.5695%
Just read 467484702 units, each unit has the size = 1
Finish reading 100%
unable to open marker file []
start to preprocessing.

Fail to allocate memory in My4DImageSimple::createImage();

It does not seem to be a good idea to allocate memory for a 30+GB image and then try to generate a graph as specified in APP2, a 128GB memory won't be a cure. Indeed I would suggest you run APP2 for smaller trunks of the data, or use sth like UltraTracer to solve the problem in divide-and-conquer way.




Originally posted by Matt Mallory:

Hello Hanchuan,

Thank you for the information. I'm a bit confused though why this tracing will not work from command line, but I am able to use app2 with user interface. I would expect the command line use to be faster and able to trace the same images that can be done with user interface?

Thank you,
Matt