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How to choose default TEASER algorithm parameters for processing #80
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Oof thanks for pointing out that inconsistency.
Any of those choices will be fine.
Igneous parameters will extract backbone without finer details. It will
cause most shorter branches to be missed.
scale 1.5 will be better for extracting small branches
scale 4 is intermediate and will emphasize backbone and take most branches.
const is in nm, so look at the calibre of the neurites you want to extract
in voxels and multiply by the resolution to get an idea of the scaling. It
should be a fraction of this size.
I'll try to harmonize this with the one kimimaro uses.
…On Sat, Jul 1, 2023, 9:30 AM s12312 ***@***.***> wrote:
In the README file on the homepage, <https://github.com/seung-lab/igneous>
kimimaro provides an example of using the Python interface with a scale of
4 and a const of 500. However, since I'm not very familiar with the TEASER
algorithm, I looked at your guide
Intuition-for-Setting-Parameters-const-and-scale
<https://github.com/seung-lab/kimimaro/wiki/Intuition-for-Setting-Parameters-const-and-scale>,
which states that "Most of the time, the defaults are fine and you
shouldn't need to touch them, with the exception of scale and const which
control the detail capture sensitivity of the procedure", meaning that in
most cases, the default parameters should be sufficient.
However, in the source code
https://github.com/seung-lab/kimimaro/blob/ffad4a641a8c668cadb6f3ec59b80b26d7f46ca2/kimimaro/intake.py#L58,
the DEFAULT_TEASAR_PARAMS specifies a scale of 1.5 and a const of 300.
Meanwhile, in the Igneous source code
https://github.com/seung-lab/igneous/blob/76a43029642fb5ad9f72b4a89bceecdaa8bb1920/igneous/task_creation/skeleton.py#L44,
the scale is set to 10 and the const is set to 10.
It seems that the default parameters in these different locations are not
very consistent. As a beginner (like me, lacking some biological
background), how should one use these parameters? For example, if I want to
process the SNEMI3D dataset, which is 1024x1024x100 (6nm x 6nm x 30nm),
what TEASAR parameters should I use?
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In the README file on the homepage, kimimaro provides an example of using the Python interface with a scale of 4 and a const of 500. However, since I'm not very familiar with the TEASER algorithm, I looked at your guide Intuition-for-Setting-Parameters-const-and-scale, which states that "Most of the time, the defaults are fine and you shouldn't need to touch them, with the exception of scale and const which control the detail capture sensitivity of the procedure", meaning that in most cases, the default parameters should be sufficient.
However, in the source code
kimimaro/kimimaro/intake.py
Line 58 in ffad4a6
It seems that the default parameters in these different locations are not very consistent. As a beginner (like me, lacking some biological background), how should one use these parameters? For example, if I want to process the SNEMI3D dataset, which is 1024x1024x100 (6nm x 6nm x 30nm), what TEASAR parameters should I use?
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