def test_mouselight_download():
mlapi = MouseLightAPI()
neurons_metadata = mlapi.fetch_neurons_metadata(filterby="soma",
filter_regions=["MOs"])
neurons = mlapi.download_neurons(neurons_metadata[0])
neurons = [neuron.create_mesh()[1] for neuron in neurons]
def test_neurons():
scene = Scene()
mlapi = MouseLightAPI()
# Fetch metadata for neurons with some in the secondary motor cortex
neurons_metadata = mlapi.fetch_neurons_metadata(filterby='soma', filter_regions=['MOs'])
# Then we can download the files and save them as a .json file
neurons = mlapi.download_neurons(neurons_metadata[:5])
scene = Scene(title='One color')
scene.add_neurons(neurons, color='salmon', display_axon=True, neurite_radius=6)
scene.render(interactive=False)
scene.close()
def test_neurons(scene):
mlapi = MouseLightAPI()
neurons_metadata = mlapi.fetch_neurons_metadata(filterby="soma",
filter_regions=["MOs"])
neurons = mlapi.download_neurons(neurons_metadata[:2])
actors = scene.add_neurons(
neurons,
color="salmon",
display_axon=False,
neurite_radius=6,
soma_radius=20,
)
actor = scene.add_neurons(
neurons[0],
color="salmon",
display_axon=False,
use_cache=True,
)
scene.add_neurons(actors,
color=None,
display_dendrites=False,
use_cache=False)
scene.add_neurons(actors, color="Reds", display_dendrites=False)
scene.add_neurons(actors,
color=["green" for i in actors],
display_dendrites=False)
scene.add_neurons(actors,
color=dict(soma="red", axon="green", dendrites="blue"))
scene.add_neurons(
actors,
color=[
dict(soma="red", axon="green", dendrites="blue") for i in actors
],
)
scene.add_neurons(actor)
def test_animated_scene():
# --------------------------------- Variables -------------------------------- #
minalpha = 0.01 # transparency of background neurons
darkcolor = "lightgray" # background neurons color
N_FRAMES = 50
N_neurons = 4 # number of neurons to show in total, if -1 all neurons are shown but it might take a while to render them at first
N_neurons_in_frame = (
2 # number of neurons to be highlighted in a given frame
)
N_frames_for_change = 15 # every N frames which neurons are shown changes
# Variables to specify camera position at each frame
zoom = np.linspace(1, 1.5, N_FRAMES)
frac = np.zeros_like(
zoom) # for camera transition, interpolation value between cameras
frac[:10] = np.linspace(0, 1, 10)
frac[10:] = np.linspace(1, 0, len(frac[10:]))
# -------------------------------- Fetch data -------------------------------- #
# Then we can download the files and save them as a .json file
ml_api = MouseLightAPI()
# Fetch metadata for neurons with some in the secondary motor cortex
neurons_metadata = ml_api.fetch_neurons_metadata(filterby="soma",
filter_regions=["MOs"])
neurons_files = ml_api.download_neurons(neurons_metadata[:N_neurons])
# ------------------------------- Create scene ------------------------------- #
scene = Scene(display_inset=False, use_default_key_bindings=True)
neurons_actors = scene.add_neurons(neurons_files,
neurite_radius=12,
alpha=0)
# Create new cameras
cam1 = buildcam(sagittal_camera)
cam2 = buildcam(
dict(
position=[-16624.081, -33431.408, 33527.412],
focal=[6587.835, 3849.085, 5688.164],
viewup=[0.634, -0.676, -0.376],
distance=51996.653,
clipping=[34765.671, 73812.327],
))
cam3 = buildcam(
dict(
position=[1862.135, -4020.792, -36292.348],
focal=[6587.835, 3849.085, 5688.164],
viewup=[0.185, -0.97, 0.161],
distance=42972.44,
clipping=[29629.503, 59872.10],
))
# ------------------------------- Create frames ------------------------------ #
# Create frames
prev_neurons = []
for step in track(np.arange(N_FRAMES),
total=N_FRAMES,
description="Generating frames..."):
if step % N_frames_for_change == 0: # change neurons every N framse
# reset neurons from previous set of neurons
for neuron in prev_neurons:
for component, actor in neuron.items():
actor.alpha(minalpha)
actor.color(darkcolor)
prev_neurons = []
# highlight new neurons
neurons = choices(neurons_actors, k=N_neurons_in_frame)
for n, neuron in enumerate(neurons):
color = colorMap(n,
"Greens_r",
vmin=-2,
vmax=N_neurons_in_frame + 3)
for component, actor in neuron.items():
actor.alpha(1)
actor.color(color)
prev_neurons.append(neuron)
# Move scene camera between 3 cameras
scene.plotter.moveCamera(cam1, cam2, frac[step])
if frac[step] == 1:
cam1 = cam3
# Update rendered window
time.sleep(0.1)
scene.render(zoom=zoom[step], interactive=False, video=True)
scene.close()
1) how to download and render neurons from the MouseLight project
using morphapi.
2) how to these neurons with a few different options to color them
You can also download data manually from the neuronbrowser website and render them by
passing the downloaded files to `scene.add_neurons`.
"""
import brainrender
brainrender.USE_MORPHOLOGY_CACHE = True
from brainrender.scene import Scene
from morphapi.morphology.morphology import Neuron
from morphapi.api.mouselight import MouseLightAPI, mouselight_structures_identifiers
# ---------------------------- 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'])
# Then we can download the files and save them as a .json file
neurons = mlapi.download_neurons(neurons_metadata[:5])
# ----------------------------- Rendering neurons ---------------------------- #
# 1 color all neurons of the same color, don't show axons
scene = Scene(title='One color')
scene.add_neurons(neurons,
color='salmon',
display_axon=False,
N_FRAMES = 250
N_neurons = 50 # number of neurons to show in total, if -1 all neurons are shown but it might take a while to render them at first
N_neurons_in_frame = 8 # number of neurons to be highlighted in a given frame
N_frames_for_change = 15 # every N frames which neurons are shown changes
# Variables to specify camera position at each frame
zoom = np.linspace(1, 1.5, N_FRAMES)
frac = np.zeros_like(
zoom) # for camera transition, interpolation value between cameras
frac[:150] = np.linspace(0, 1, 150)
frac[150:] = np.linspace(1, 0, len(frac[150:]))
# -------------------------------- Fetch data -------------------------------- #
# Then we can download the files and save them as a .json file
ml_api = MouseLightAPI()
# Fetch metadata for neurons with some in the secondary motor cortex
neurons_metadata = ml_api.fetch_neurons_metadata(filterby="soma",
filter_regions=["MOs"])
neurons_files = ml_api.download_neurons(neurons_metadata[:N_neurons])
# ------------------------------- Create scene ------------------------------- #
scene = Scene(display_inset=False, use_default_key_bindings=True)
neurons = scene.add_neurons(neurons_files, neurite_radius=12, alpha=0)
# Make all neurons background
for neuron in neurons:
for mesh in neuron.values():
mesh.alpha(minalpha)
def test_imports():
aba = ABA()
mlapi = MouseLightAPI()
from brainrender import Scene
from brainrender.actors import make_neurons, Neuron
from morphapi.api.mouselight import MouseLightAPI
# Create a brainrender scene
scene = Scene(title="neurons")
# Add a neuron from file
scene.add(Neuron("examples/data/neuron1.swc"))
# Download neurons data with morphapi
mlapi = MouseLightAPI()
neurons_metadata = mlapi.fetch_neurons_metadata(filterby="soma",
filter_regions=["MOs"])
to_add = [neurons_metadata[47], neurons_metadata[51]]
neurons = mlapi.download_neurons(to_add)
neurons = scene.add(*make_neurons(*neurons, neurite_radius=12))
# Render!
scene.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.morphology.morphology import Neuron
from morphapi.api.mouselight import MouseLightAPI, mouselight_structures_identifiers
# ---------------------------- 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'])
# Then we can download the files and save them as a .json file
neurons = mlapi.download_neurons(
neurons_metadata[:50]) # 50 neurons, might take a while the first time
# ----------------------------- Rendering neurons ---------------------------- #
# Create a custom colormap between 3 colors
colors = makePalette(len(neurons), 'salmon', 'lightgreen')
# Create scene