Connectomes

NiiVue considers connectomes as a special class of meshes. While most meshes have fixed vertex positions (e.g. a brain is considered to have a fixed size), the radius of connectome nodes and edges can be scaled dynamically. The notebook mirrors the JavaScript connectome web page.

TODO: full notebook requires future ipyniivue: legend_line_thickness, edge_min, edge_max

import ipywidgets as widgets
from IPython.display import display
from ipyniivue import NiiVue
nv = NiiVue()

nv.load_volumes([{"path": "../images/mni152.nii.gz"}])
nv.load_meshes([
    {"path": "../images/connectome.jcon"}
     ])

nv.set_clip_plane(0.1, 0, 135)
nv.opts.mesh_xray = 0.1

# Create UI

edge_scale_slider = widgets.FloatSlider(
    value=1,
    min=0.5,
    max=3,
    step=0.1,
    description="Edge",
    readout=False
)

def on_edge_scale_change(change):
    """Set size of edges."""
    nv.meshes[0].edge_scale = change["new"]

edge_scale_slider.observe(on_edge_scale_change, names="value")

node_scale_slider = widgets.FloatSlider(
    value=3,
    min=0.5,
    max=6,
    step=0.1,
    description="Node",
    readout=False
)

def on_node_scale_change(change):
    """Set size of nodes."""
    nv.meshes[0].node_scale = change["new"]

node_scale_slider.observe(on_node_scale_change, names="value")

legend_slider = widgets.IntSlider(
    value=3,
    min=0,
    max=12,
    description="Legend lines",
    readout=False,
    disabled=True
)

def on_legend_change(change):
    """Set size of legend lines."""
    nv.meshes[0].legend_line_thickness = change["new"]

legend_slider.observe(on_legend_change, names="value")

stat_range = widgets.FloatRangeSlider(
    value=[40, 80],
    min=0.1,
    max=120.0,
    step=0.1,
    continuous_update=True,
    description="Threshold:",
    readout=False
)

def on_stat_change(change):
    """Set threshold for statistical overlay."""
    low, high = change["new"]    # extract the two values
    nv.volumes[0].cal_min = low
    nv.volumes[0].cal_max = high 

stat_range.observe(on_stat_change, names="value")

# Display
controls = widgets.HBox([edge_scale_slider, node_scale_slider, legend_slider, stat_range])

display(widgets.VBox([controls, nv]))