MetaCell / MetaCell/NetPyNE-UI

3D positions of cells being displayed incorrectly

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Dominant language
JavaScript
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Description

This [NeuroML file](https://github.com/OpenSourceBrain/NetPyNEShowcase/blob/master/NeuroML2/TwoCells/TwoCell.net.nml#L44) contains 2 cells, a basket cell on the left (at the origin) and a pyramidal cell on the right (at ``). The soma of the pyramidal cell should be below the basket cell as shown in this export of the cell from NML (use: `pynml -png TwoCell.net.nml`, see [here](https://docs.neuroml.org/Userdocs/VisualisingNeuroMLModels.html#view-the-3d-structure-of-your-model)):

![TwoCell net](https://github.com/MetaCell/NetPyNE-UI/assets/1556687/daa8ad79-b74a-447f-a2e8-b8a73a0ca630)

However when this is imported into NetPyNE (e.g. by creating a workspace from https://v2.opensourcebrain.org/repositories/14 and importing the NML file above) the soma is above the basket cell (left below):

![Screenshot 2023-12-19 at 16 19 43](https://github.com/MetaCell/NetPyNE-UI/assets/1556687/ce7764de-3757-4c51-b512-fc9b1c5b81db)

The correct position seems to be in netpyne's memory, as the right panel shows its own 3D view, with the yellow dot on the right for the pyramidal cell at the right locaion.

Also a json file exported from the neuroml version has the right location: https://github.com/OpenSourceBrain/NetPyNEShowcase/blob/master/NetPyNE/TwoCells/LEMS_TwoCell_netpyne_data.json#L29

Is it possibly the issue is to do with the `"ynorm": -2.0` linked above, as the y position looks like it is wrongly multiplied by -2?

Contributor guide

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Research direction

Reproduce the issue by creating a workspace from the linked repository and importing NeuroML2/TwoCells/TwoCell.net.nml. Compare the displayed cell coordinates with the NeuroML export and NetPyNE/TwoCells/LEMS_TwoCell_netpyne_data.json, especially the pyramidal cell's y position and ynorm value. Done means the imported 3D view places the pyramidal soma below the basket cell consistently with the source data.

Written by the indexing model from the issue text.

Assessment

Tech stack
javascript
Domain
computer-graphics, frontend
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
42/100

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