help > Intensity profile in 3D
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May 13, 2019  08:05 AM | Sarah Goethals
Intensity profile in 3D
Hi,

I want to measure the intensity profile along axons in 3D stacks. For that, I open the stacks in the 3D viewer, right-click and select "1-right stroke to define a 3D curve (v2b)". Then I draw the line and right-click on it but when I select "neuron-segment intensity profile", an error message appears:
"
Invalid data type (only uint8 is supported now) in proj_trace_profileNeuronSeg()
"
So I can't obtain the intensity profile along my curve. Do you have an idea of how to solve that problem? It would help me a lot.

Thanks in advance,

Sarah
May 13, 2019  11:05 PM | Zhi Zhou
RE: Intensity profile in 3D
Please convert your image to be uint8 first before using this function. You can find multiple conversion options under "Image/Data" --> "image type".



Originally posted by Sarah Goethals:
Hi,

I want to measure the intensity profile along axons in 3D stacks. For that, I open the stacks in the 3D viewer, right-click and select "1-right stroke to define a 3D curve (v2b)". Then I draw the line and right-click on it but when I select "neuron-segment intensity profile", an error message appears:
"
Invalid data type (only uint8 is supported now) in proj_trace_profileNeuronSeg()
"
So I can't obtain the intensity profile along my curve. Do you have an idea of how to solve that problem? It would help me a lot.

Thanks in advance,

Sarah
May 14, 2019  12:05 AM | Sarah Goethals
RE: Intensity profile in 3D
Ok, I will try that, thanks for the rapide answer.

Sarah
May 14, 2019  11:05 PM | Sarah Goethals
RE: Intensity profile in 3D
Hi,

I changed the image type (either using "linear rescale ..." or "saturate top/bottom ...") and now when I want to measure the intensity profile, Vaa3d closes. Do you have any idea of how I can solve that? The application closes just after clicking on "neuron-segment intensity profile". It happens when I use "global optimal" and "bbox" to trace the neuron segment.
I am using Mac OS El Capitan 10.11 with Vaa3d 3.2. 

Thanks,

Sarah
May 15, 2019  12:05 AM | Zhi Zhou
RE: Intensity profile in 3D
Please try our newer versions at https://github.com/Vaa3D/release. If it still doesn't work, please send the image for us to test. Thanks.
May 16, 2019  05:05 AM | Sarah Goethals
RE: Intensity profile in 3D
The newer version don't work (the application does not want to open) but I did what is suggested here https://www.nitrc.org/forum/forum.php?thread_id=7925&forum_id=1553 and it works.

Sarah