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feat: add interactive3d viewer images
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sanjayankur31 committed Oct 27, 2023
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20 changes: 15 additions & 5 deletions source/Userdocs/VisualisingCells.md
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Expand Up @@ -11,8 +11,7 @@ E.g., {ref}`NetPyNE and NetPyNE-UI <userdocs:supporting:apps:netpyne>`, {ref}`ne
## Visualising morphology of multi-compartmental cell models

Multi-compartmental cells can be visualised using the [plot_2D](https://pyneuroml.readthedocs.io/en/development/pyneuroml.plot.html#pyneuroml.plot.PlotMorphology.plot_2D) and [plot_interactive_3D](https://pyneuroml.readthedocs.io/en/development/pyneuroml.plot.html#pyneuroml.plot.PlotMorphology.plot_interactive_3D) methods included in {ref}`pyNeuroML <pyNeuroML>`.
(Note that the 3D plotter, while interactive, may require considerable hardware resources to plot larger, more complex cell morphologies).

This functionality is also exposed via the `pynml-plotmorph` command line tool.

```{figure} ../images//test_morphology_plot_2d_Cell_497232312_cell_nml_xy.png
:alt: Morphology of example cell plotted with `plot_2D`
Expand All @@ -21,12 +20,23 @@ Multi-compartmental cells can be visualised using the [plot_2D](https://pyneurom
Morphology of example cell plotted with `plot_2D` in the X-Y plane.
```
```{figure} ../images//test_morphology_plot_3d_Cell_497232312_cell_nml.png
:alt: Morphology of example cell plotted with `plot_3D`

```{figure} ../images/pynml-plotmorph-1.png
:alt: Morphology of example cell visualised with `plot_interactive_3D`
:align: center
:width: 70%
Interactive visualisation of morphology of an example cell `plot_interactive_3D`.
```

These tools also allow plotting of networks.

```{figure} ../images/pynml-plotmorph-2.png
:alt: A network visualised with `plot_interactive_3D`
:align: center
:width: 70%
Interactive visualisation of morphology of an example cell `plot_3D` in a web-browser.
Interactive visualisation of a network with `plot_interactive_3D`.
```

(userdocs:visualising_cells:morph:nmldb)=
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