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# Visualizing MRI Volume Slices in Python

How to create an plotly animation with slider that cycles through MRI cross-sections of a human brain.

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#### Visualization of MRI volume slices¶

In [1]:
# Import data
import time
import numpy as np

from skimage import io

volume = vol.T
r, c = volume[0].shape

# Define frames
import plotly.graph_objects as go
nb_frames = 68

fig = go.Figure(frames=[go.Frame(data=go.Surface(
z=(6.7 - k * 0.1) * np.ones((r, c)),
surfacecolor=np.flipud(volume[67 - k]),
cmin=0, cmax=200
),
name=str(k) # you need to name the frame for the animation to behave properly
)
for k in range(nb_frames)])

# Add data to be displayed before animation starts
z=6.7 * np.ones((r, c)),
surfacecolor=np.flipud(volume[67]),
colorscale='Gray',
cmin=0, cmax=200,
colorbar=dict(thickness=20, ticklen=4)
))

def frame_args(duration):
return {
"frame": {"duration": duration},
"mode": "immediate",
"fromcurrent": True,
"transition": {"duration": duration, "easing": "linear"},
}

sliders = [
{
"len": 0.9,
"x": 0.1,
"y": 0,
"steps": [
{
"args": [[f.name], frame_args(0)],
"label": str(k),
"method": "animate",
}
for k, f in enumerate(fig.frames)
],
}
]

# Layout
fig.update_layout(
title='Slices in volumetric data',
width=600,
height=600,
scene=dict(
zaxis=dict(range=[-0.1, 6.8], autorange=False),
aspectratio=dict(x=1, y=1, z=1),
),
{
"buttons": [
{
"args": [None, frame_args(50)],
"label": "&#9654;", # play symbol
"method": "animate",
},
{
"args": [[None], frame_args(0)],
"label": "&#9724;", # pause symbol
"method": "animate",
},
],
"direction": "left",