Plotting brain region values on circular flatmap

This example walks through various ways to overlay brain region values on a circular flatmap

The circular flatmap

The circular flatmap is obtained by sampling the volume using concentric circles through the brain.

[1]:

from iblatlas.flatmaps import FlatMap
flmap_cr = FlatMap(flatmap='circles')

[2]:

# Display the concentric circles used in flatmap
ax = flmap_cr.plot_top(volume='image')
ax.plot(flmap_cr.ml_scale * 1e6, flmap_cr.ap_scale * 1e6)

/opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/site-packages/iblatlas/atlas.py:172: RuntimeWarning: invalid value encountered in cast
  ii = np.array(np.round(i)).astype(int)

Out[2]:

[<matplotlib.lines.Line2D at 0x7f8938e8b880>]

../_images/notebooks_external_atlas_circular_pyramidal_flatmap_5_2.png

This results in a flatmap that can be displayed in the following way

[3]:

import matplotlib.pyplot as plt
fig, ax = plt.subplots(figsize=(18,4))
flmap_cr.plot_flatmap(ax)

Out[3]:

<Axes: >

../_images/notebooks_external_atlas_circular_pyramidal_flatmap_7_1.png

It is also possible to display this flatmap such that each circle is stacked on top of eachother. For this, the pyramid flatmap should be used

[4]:

# Instantiate flatmap with circles arranged vetically on top of eachother
flmap_py = FlatMap(flatmap='pyramid')

[5]:

fig, ax = plt.subplots(figsize=(8, 8))
flmap_py.plot_flatmap(ax=ax)

Out[5]:

<Axes: >

../_images/notebooks_external_atlas_circular_pyramidal_flatmap_10_1.png

Data preparation

In order to plot brain regions values on the flatmap an array of acronyms and an array of values corresponding to each acronym must be provided. A detailed overview of how to prepare your data can be found here

[6]:

import numpy as np
# prepare array of acronyms
acronyms = np.array(['VPM', 'PO', 'LP', 'CA1', 'DG-mo', 'VISa5', 'SSs5'])
# assign data to each acronym
values = np.arange(acronyms.size)

[7]:

from iblatlas.regions import BrainRegions
br = BrainRegions()
# prepare array of acronyms with beryl mapping
acronyms_beryl = np.unique(br.acronym2acronym(acronyms, mapping='Beryl'))
values_beryl = np.arange(acronyms_beryl.size)

[8]:

# prepare different values for left and right hemipshere for Beryl acronyms
values_beryl_lh = np.random.randint(0, 10, acronyms_beryl.size)
values_beryl_rh = np.random.randint(0, 10, acronyms_beryl.size)
values_beryl_lr = np.c_[values_beryl_lh, values_beryl_rh]

Examples

[9]:

from iblatlas.plots import plot_scalar_on_flatmap
# Plot region values on the left hemisphere of circle flatmap overlaid on brain region boundaries using Allen mapping
fig, ax = plt.subplots(figsize=(18,4))
fig, ax = plot_scalar_on_flatmap(acronyms, values, hemisphere='left', mapping='Allen', flmap_atlas=flmap_cr, ax=ax)

../_images/notebooks_external_atlas_circular_pyramidal_flatmap_17_0.png

[10]:

# Plot region values on the both hemispheres of circle flatmap overlaid on the dwi Allen image  using Beryl mapping
fig, ax = plt.subplots(figsize=(18,4))
fig, ax = plot_scalar_on_flatmap(acronyms_beryl, values_beryl, hemisphere='both', mapping='Beryl', background='image',
                                 cmap='Reds', flmap_atlas=flmap_cr,  ax=ax)

../_images/notebooks_external_atlas_circular_pyramidal_flatmap_18_0.png

[11]:

# Plot region values on the right hemisphere of pyramidal flatmap overlaid on the dwi Allen image using Allen mapping
fig, ax = plt.subplots(figsize=(8,8))
fig, ax = plot_scalar_on_flatmap(acronyms, values, hemisphere='right', mapping='Allen', background='image',
                                 cmap='Reds', flmap_atlas=flmap_py,  ax=ax)

../_images/notebooks_external_atlas_circular_pyramidal_flatmap_19_0.png

[12]:

# Plot two column region values on the both hemispheres of pyramidal flatmap overlaid on brain region boundaries
# using Beryl mapping
fig, ax = plt.subplots(figsize=(8,8))
fig, ax = plot_scalar_on_flatmap(acronyms_beryl, values_beryl_lr, hemisphere='both', mapping='Beryl',
                                 background='boundary', cmap='Blues', flmap_atlas=flmap_py,  ax=ax)

../_images/notebooks_external_atlas_circular_pyramidal_flatmap_20_0.png