Slice View

This module provides tools for visualizing 2D brain slice views with optional region annotations and angle offsets.

Basic Usage

Use get_slice_view() to create a slice view and select a plane at a specific index:

from neuralib.atlas.view import get_slice_view

# Get a reference view in coronal plane at 10µm resolution
view = get_slice_view('reference', plane_type='coronal', resolution=10)

# Select a plane at slice index 700
plane = view.plane_at(700)

# Plot with region boundaries
plane.plot(boundaries=True)

View types:

reference: Grayscale reference image
annotation: Color-coded region annotation

Plane types:

coronal: Front-to-back sections
sagittal: Left-to-right sections
transverse: Top-to-bottom sections (horizontal)

Angle Offset

Apply angular offsets to simulate angled slice cuts using with_angle_offset():

ML offset in coronal slice

Use deg_x for medial-lateral axis rotation:

import matplotlib.pyplot as plt
from neuralib.atlas.view import get_slice_view

slice_index = 700
plane = get_slice_view('reference', plane_type='coronal', resolution=10).plane_at(slice_index)

_, ax = plt.subplots(ncols=2, figsize=(20, 10))

plane.plot(ax=ax[0], boundaries=True)
ax[0].set_title('without offset')

plane.with_angle_offset(deg_x=10).plot(ax=ax[1], boundaries=True)
ax[1].set_title('+10 degree ML offset')

DV offset in sagittal slice

Use deg_y for dorsal-ventral axis rotation:

slice_index = 500
plane = get_slice_view('annotation', plane_type='sagittal', resolution=10).plane_at(slice_index)

_, ax = plt.subplots(ncols=2, figsize=(20, 10))

plane.plot(ax=ax[0], boundaries=True)
ax[0].set_title('without offset')

plane.with_angle_offset(deg_y=20).plot(ax=ax[1], boundaries=True)
ax[1].set_title('+20 degree DV offset')

Region Annotation

Highlight specific brain regions using the annotation_region parameter:

from neuralib.atlas.data import get_children
from neuralib.atlas.view import get_slice_view

slice_index = 900
plane = get_slice_view('reference', plane_type='coronal', resolution=10).plane_at(slice_index)

_, ax = plt.subplots(ncols=2, figsize=(20, 10))

# Annotate CA1 and Primary Visual Cortex
plane.plot(ax=ax[0], boundaries=True, annotation_region=['CA1', 'VISp'])

# Get all VISp subregions (layers)
primary_visual_layers = get_children('VISp', dataframe=False)
print(primary_visual_layers)  # ['VISp1', 'VISp2/3', 'VISp4', 'VISp5', 'VISp6a', 'VISp6b']

# Annotate with offset view and detailed tree regions
plane.with_angle_offset(deg_x=10).plot(ax=ax[1], boundaries=True, annotation_region=['CA1'] + primary_visual_layers)

Annotation in transverse view

slice_index = 300
plane = get_slice_view('reference', plane_type='transverse', resolution=10).plane_at(slice_index)

_, ax = plt.subplots(ncols=2, figsize=(20, 10))

# Default colormap
plane.plot(ax=ax[0], annotation_region=['ACA', 'LP'])

# Custom colormap with boundaries
plane.plot(ax=ax[1], annotation_region=['SS', 'MO'], annotation_cmap='PiYG', boundaries=True)

Max Projection

Generate a maximum intensity projection across all slices for specified regions:

from neuralib.atlas.data import get_children
from neuralib.atlas.view import get_slice_view

view = get_slice_view('reference', plane_type='transverse', resolution=10)

_, ax = plt.subplots()

# Get all visual area subregions
regions = get_children('VIS')
print(regions)  # ['VISal', 'VISam', 'VISl', 'VISli', 'VISp', 'VISpl', 'VISpm', 'VISpor']

# Plot max projection for all visual areas
view.plot_max_projection(ax, annotation_regions=regions)