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brainrender.DEFAULT_STRUCTURE_ALPHA
brainrender.INJECTION_VOLUME_SIZE
brainrender.TRACTO_RADIUS
brainrender.TRACTO_ALPHA
brainrender.TRACTO_RES
brainrender.TRACT_DEFAULT_COLOR
brainrender.INJECTION_DEFAULT_COLOR
brainrender.STREAMLINES_RESOLUTION
brainrender.INJECTION_VOLUME_SIZE
brainrender.TRACTO_RADIUS
brainrender.TRACTO_ALPHA
brainrender.TRACTO_RES
brainrender.TRACT_DEFAULT_COLOR
brainrender.INJECTION_DEFAULT_COLOR
brainrender.STREAMLINES_RESOLUTION
brainrender.SHADER_STYLE
brainrender.VERBOSE
brainrender.HDF_SUFFIXES
brainrender.DEFAULT_HDF_KEY
brainrender.reset_defaults()
"""
This example shows how to cut selected actors in the scene using a
custom plane
"""
import brainrender
brainrender.SHADER_STYLE = "cartoon"
from brainrender.scene import Scene
scene = Scene(use_default_key_bindings=True)
# Add some actors
th = scene.add_brain_regions(["STR", "TH"], alpha=0.5)
# Specify position, size and orientation of the plane
pos = scene.atlas._root_midpoint
sx, sy = 15000, 15000
norm = [0, 1, 1]
plane = scene.atlas.get_plane_at_point(
pos, norm=norm, sx=sx, sy=sy, color="lightblue"
)
"""
This example shows how to add 3D text to your scenes
"""
import brainrender
brainrender.SHADER_STYLE = "cartoon"
from brainrender.scene import Scene
from brainrender.colors import makePalette
from vedo import Text
camera = dict(
{
"position": (4.58173814842751, 1.3170832519052862, 28.807539941401348),
"focal": (5.63320729136467, 0.0, 0.13752250373363495),
"viewup": (
0.008857944291024357,
0.9989221022772287,
-0.04556501294830602,
),
"distance": 28.719508970857582,
"""
This tutorial shows how download and rendered afferent mesoscale projection data
using the AllenBrainAtlas (ABA) and Scene classes
"""
import brainrender
brainrender.SHADER_STYLE = "cartoon"
from brainrender.scene import Scene
from brainrender.atlases.mouse import ABA
# Create a scene
scene = Scene(title="tractography")
# Get the center of mass of the region of interest
p0 = scene.atlas.get_region_CenterOfMass("ZI")
# Get projections to that point
analyzer = ABA()
tract = analyzer.get_projection_tracts_to_target(p0=p0)
# Add the brain regions and the projections to it
scene.add_brain_regions(["ZI"], alpha=0.4, use_original_color=True)
"""
This example shows how to crate an animate scene where
over a number of frames:
- Different sets of streamlines data from the mouse connectome project
- The camera moves around
"""
import brainrender
brainrender.WHOLE_SCREEN = False
brainrender.SHADER_STYLE = "cartoon"
brainrender.ROOT_ALPHA = 0.1
from brainrender.scene import Scene
import time
import numpy as np
from random import choices
from rich.progress import track
from brainrender.Utils.camera import (
top_camera,
buildcam,
sagittal_camera,
)
"""
This example shows how to create a scene that has a cartoony look
(good for schematics and illustrations)
"""
import brainrender
brainrender.SHADER_STYLE = "cartoon" # gives actors a flat shading
from brainrender.scene import Scene
scene = Scene()
th = scene.add_brain_regions("TH", alpha=0.5)
# Create a black line around each actor
scene.add_silhouette(scene.root)
scene.add_silhouette(th, lw=3)
scene.render()
import brainrender
brainrender.WHOLE_SCREEN = True
brainrender.SHADER_STYLE = "cartoon"
from brainrender.scene import Scene
from brainrender.animation.video import BasicVideoMaker
scene = Scene(display_inset=False, camera="sagittal")
scene.add_brain_regions(["MOs"])
scene.add_neurons("Examples/example_files/neuron1.swc", color="black")
vmkr = BasicVideoMaker(scene)
vmkr.make_video(azimuth=1, niters=36, duration=30, save_name="test")
import brainrender
brainrender.SHADER_STYLE = "cartoon"
brainrender.ROOT_ALPHA = 0.2
from brainrender.scene import Scene
from brainrender.atlases.ccustom_atlases.insects_brains_db import (
IBDB,
) # ! this class is the atlas for insects brains
"""
In this tutorial you can see how to use brainrender to fetch
and render 3D rendering of brain regions from a number of insects brains.
All data is hosted by: https://insectbraindb.org/app/
Please read their terms of use (https://insectbraindb.org/app/terms)
Also please refer to the website to find the original source of these datasets
You can also visualize these data interactively at: https://insectbraindb.org/app/three;controls=true;mode=species
"""
This example shows how download neurons from the
mouselight datase with morphapi and render
them with a custom colors palette
"""
import brainrender
brainrender.SHADER_STYLE = "cartoon"
brainrender.ROOT_ALPHA = 0.3
brainrender.BACKGROUND_COLOR = "blackboard"
from brainrender.scene import Scene
from brainrender.colors import makePalette
from morphapi.api.mouselight import MouseLightAPI
# ---------------------------- Downloading neurons --------------------------- #
mlapi = MouseLightAPI()
# Fetch metadata for neurons with some in the secondary motor cortex
neurons_metadata = mlapi.fetch_neurons_metadata(
filterby="soma", filter_regions=["MOs"]
def main(regions, atlas=None, cartoon=False, debug=False, file=None):
# Set look
if cartoon:
brainrender.SHADER_STYLE = "cartoon"
# Create scene
scene = Scene(atlas=atlas)
# Add brain regions
if regions is not None and len(regions) > 0:
acts = scene.add_brain_regions(list(regions))
# Add silhouettes
if cartoon:
if isinstance(acts, list):
scene.add_silhouette(*acts)
else:
scene.add_silhouette(acts)
# Add data from file