def test_mouselight():
from brainrender.Utils.MouseLightAPI.mouselight_api import MouseLightAPI
from brainrender.Utils.MouseLightAPI.mouselight_info import mouselight_api_info, mouselight_fetch_neurons_metadata
# Fetch metadata for neurons with some in the secondary motor cortex
neurons_metadata = mouselight_fetch_neurons_metadata(
filterby='soma', filter_regions=['MOs'])
# Then we can download the files and save them as a .json file
ml_api = MouseLightAPI()
neurons_files = ml_api.download_neurons(
neurons_metadata[:2]
) # just saving the first couple neurons to speed things up
# Show neurons and ZI in the same scene:
scene = Scene()
scene.add_neurons(
neurons_files,
soma_color='orangered',
dendrites_color='orangered',
axon_color='darkseagreen',
neurite_radius=8
) # add_neurons takes a lot of arguments to specify how the neurons should look
# make sure to check the source code to see all available optionsq
scene.add_brain_regions(['MOs'], alpha=0.15)
scene.render(camera='coronal')
def test_neurons():
scene = Scene()
mlapi = MouseLightAPI()
neurons_metadata = mouselight_fetch_neurons_metadata(filterby='soma', filter_regions=['MOs'])
neurons_files = mlapi.download_neurons(neurons_metadata[:2])
parser = NeuronsParser(scene=scene,
color_neurites=True, axon_color="antiquewhite",
soma_color="darkgoldenrod", dendrites_color="firebrick")
neurons, regions = parser.render_neurons(neurons_files)
scene.add_neurons(neurons_files, color_neurites=False, random_color="jet", display_axon_regions=False)
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 brainrender.Utils.MouseLightAPI.mouselight_api import MouseLightAPI
from brainrender.Utils.MouseLightAPI.mouselight_info import mouselight_api_info, mouselight_fetch_neurons_metadata
# Fetch metadata for neurons with some in the secondary motor cortex
neurons_metadata = mouselight_fetch_neurons_metadata(filterby='soma',
filter_regions=['MOs'])
# Then we can download the files and save them as a .json file
ml_api = MouseLightAPI()
neurons_files = ml_api.download_neurons(
neurons_metadata[:2]
) # just saving the first couple neurons to speed things up
# Show neurons and ZI in the same scene:
scene = Scene()
scene.add_neurons(
neurons_files,
soma_color='orangered',
dendrites_color='orangered',
axon_color='darkseagreen',
neurite_radius=8
) # add_neurons takes a lot of arguments to specify how the neurons should look
# make sure to check the source code to see all available optionsq
import brainrender
brainrender.SHADER_STYLE = 'cartoon'
from brainrender.scene import Scene
from brainrender.Utils.ABA.connectome import ABA
from brainrender.Utils.MouseLightAPI.mouselight_info import mouselight_api_info, mouselight_fetch_neurons_metadata
from brainrender.Utils.MouseLightAPI.mouselight_api import MouseLightAPI
from brainrender.Utils.parsers.streamlines import StreamlinesAPI
from brainrender.Utils.data_io import listdir
from brainrender.colors import get_n_shades_of
aba = ABA()
streamlines_api = StreamlinesAPI()
mlapi = MouseLightAPI()
# ---------------------------------------------------------------------------- #
# DEFINE A FUNCTION FOR EACH EXAMPLE SCENE #
# ---------------------------------------------------------------------------- #
def BrainRegionsScene():
scene = Scene()
scene.add_brain_regions(['TH', 'VP'], use_original_color=True, alpha=1)
act = scene.actors['regions']['TH']
scene.edit_actors([act], wireframe=True)
scene.render()
def test_imports():
aba = ABA()
streamlines_api = StreamlinesAPI()
mlapi = MouseLightAPI()
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 -------------------------------- #
# Fetch metadata for neurons with some in the secondary motor cortex
neurons_metadata = mouselight_fetch_neurons_metadata(filterby='soma',
filter_regions=['MOs'])
# Then we can download the files and save them as a .json file
ml_api = MouseLightAPI()
neurons_files = ml_api.download_neurons(neurons_metadata[:N_neurons])
# ------------------------------- Create scene ------------------------------- #
scene = Scene(display_inset=False, use_default_key_bindings=True)
root = scene.actors['root']
scene.add_neurons(neurons_files, random_color=True, neurite_radius=12, alpha=0)
# Make all neurons background
for neuron in scene.actors['neurons']:
for mesh in neuron.values():
mesh.alpha(minalpha)
mesh.color(darkcolor)
# Create new cameras