Automatic mesh generator: can't figure out how to run neuroglancer

I have tried few examples so far and couldn’t make them work in my case:

1. Grayscale raw image:

raw = np.fromfile('raw.bin',dtype=np.uint16).reshape([1200,880,930])

1. Segmented companion:

segs = np.fromfile('segs.bin',dtype=np.uint32).reshape(raw.shape)

But I don’t know where to start from in order to make neuroglancer to work in my case.

Could anyone please help me?

Thanks in Advance, Anar.

[jbms]

Regarding nyroglancer, I think it unfortunately does not support the automatic meshing.

The error you list at the top of init takes 3 positional arguments is a recent breakage in sockjs-tornado due to the release of tornado 5.0 just a few days ago. https://github.com/mrjoes/sockjs-tornado/issues/113

To fix that, you could either downgrade tornado to 4.5.3 via pip install tornado==4.5.3

or install this version of sockjs tornado from github.

https://github.com/mathben/sockjs-tornado/tree/fix_tornado_5.0_%23113

You can do that with this command: pip install ‘git+git://github.com/mathben/sockjs-tornado@212ba27’ --upgrade

[jbms]

Use the Slices checkbox or press s.

On Thu, May 17, 2018, 08:34 Anar Z. Yusifov [e-mail] wrote:

Thank you, @jbms https://github.com/jbms for your help! How to remove visualization of orthogonal 3D planes? The reason I need it is that I can browse through my data in 3 other windows but would like to see 3D generated object clearly in my 3D view without panels going into my sight. May be I can set transparency for the panels or somehow disable them in 3D view?

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