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knossos-project / knossos

KNOSSOS is a software tool for the visualization and annotation of 3D image data and was developed for the rapid reconstruction of neural morphology and connectivity.
https://knossos.app
GNU General Public License v2.0
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"Scripting" menu item required for Syconn2 but grayed out #508

Closed erjel closed 1 year ago

erjel commented 1 year ago

Hi,

I would like to use Knossos for the visualization of a Syconn2 workflow. Unfortunately the "Scriptiong" menu item is grayed out.

Background: According to the Syconn2 documentation I need the following steps:

  1. Analysis results (download link for reference)
  2. Start the server with syconn.server --working_dir=<my results>
    • I created the environment with this conda env file and a following
    • pip install git+https://github.com/ada52/SyConn.git@2e59d9a1c90bd12531c5aac96f6f96ddebdf5e9f
  3. Download and install the nightly build of KNOSSOS
  4. Open the segmentation data in KNOSSOS
  5. Add syconn/kplugin/syconn_knossos_viewer.py in the Scripting menu

Unfortunately, the menu is grayed out .. therefore I cannot proceed ...

Any ideas, why this is the case?

Best wishes and thank you in advance! Eric

erjel commented 1 year ago

Switching to the stable release (version 5.1) solved this issue for me.

Optiligence commented 1 year ago

Hi, the difference might be that v5.1 integrates with python 2.7 whereas the nightly is using python 3.11 at the moment. There might also be other issues that influence if it works. It’s a little more complicated with the regular binary incompatible python 3 releases. It should complain on startup though, did it?

erjel commented 1 year ago

All I can say that there was no, error message on startup...