MRI slices tutorial

python/visualizing-mri-volume-slices.md

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+---
+jupyter:
+  jupytext:
+    notebook_metadata_filter: all
+    text_representation:
+      extension: .md
+      format_name: markdown
+      format_version: '1.1'
+      jupytext_version: 1.2.3
+  kernelspec:
+    display_name: Python 3
+    language: python
+    name: python3
+  language_info:
+    codemirror_mode:
+      name: ipython
+      version: 3
+    file_extension: .py
+    mimetype: text/x-python
+    name: python
+    nbconvert_exporter: python
+    pygments_lexer: ipython3
+    version: 3.7.3
+  plotly:
+    description: How to create an plotly animation with slider that cycles through
+      MRI cross-sections of a human brain.
+    display_as: animations
+    has_thumbnail: true
+    ipynb: ~notebook_demo/190
+    language: python
+    layout: user-guide
+    name: Visualizing MRI Volume Slices
+    order: 4
+    page_type: example_index
+    permalink: python/visualizing-mri-volume-slices/
+    thumbnail: thumbnail/brain-mri-animation_square.gif
+    title: Visualizing MRI Volume Slices | plotly
+---
+
+#### Visualization of MRI volume slices
+
+```python
+# Import data
+import time
+import numpy as np
+
+from skimage import io
+
+vol = io.imread("https://s3.amazonaws.com/assets.datacamp.com/blog_assets/attention-mri.tif")
+volume = vol.T
+r, c = volume[0].shape
+
+# Visualize data
+import plotly.graph_objects as go
+
+nb_frames = 68
+
+# Define frames
+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])
+    ))
+    for k in range(nb_frames)])
+
+# Add data to be displayed before animation starts
+fig.add_trace(go.Surface(
+    z=6.7 * np.ones((r, c)),
+    surfacecolor=np.flipud(volume[67]),
+    colorscale='Gray',
+    colorbar=dict(thickness=20, ticklen=4)
+    ))
+
+# Sliders
+sliders=[
+    dict(
+        steps=[dict(method='animate',
+                    args= [None, dict(fromcurrent=True, mode='immediate', transition=dict(duration=0))
+                          ],
+                    label='{:d}'.format(k+1)) 
+               for k in range(nb_frames)],
+        transition= dict(duration=0),
+    )
+]
+
+# 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),
+                    ),
+         updatemenus=[
+             dict(type='buttons',
+                  buttons=[dict(label='Play',
+                                method='animate',
+                                args=[None])])
+         ],
+         sliders=sliders
+)
+
+fig.show()
+```
+
+#### Credit:
+All credit goes to Emilia Petrisor for this excellent animation!
+
+Here's where you can find her:
+- Her [Twitter](https://twitter.com/mathinpython) under the handle `@mathinpython`
+- Her [GitHub Page](https://github.com/empet) with Username `empet`
+
+
+#### Reference
+For additional information and help setting up a slider in an animation, see https://plot.ly/python/gapminder-example/. For more documentation on creating animations with Plotly, see https://plot.ly/python/#animations.
+