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)
set_camera(scene)
scene.render()
def StreamlinesScene():
streamlines_files, data = streamlines_api.download_streamlines_for_region("PAG")
scene = Scene()
scene.add_streamlines(data[3], color="powderblue", show_injection_site=False, alpha=.3, radius=10)
scene.add_brain_regions(['PAG'], use_original_color=False, colors='powderblue', alpha=.9)
mos = scene.actors['regions']['PAG']
scene.edit_actors([mos], wireframe=True)
set_camera(scene)
scene.render()
def NeuronsScene2():
scene = Scene()
neurons_metadata = mouselight_fetch_neurons_metadata(filterby='soma', filter_regions=['MOp5'])
neurons_files = download_neurons(neurons_metadata[2:6])
scene.add_neurons(neurons_files, soma_color='deepskyblue', force_to_hemisphere="right")
streamlines_files, data = streamlines_api.download_streamlines_for_region("MOp")
scene.add_streamlines(data[:1], color="palegreen", show_injection_site=False, alpha=.2, radius=10)
set_camera(scene)
scene.render()
def NeuronsScene(show_regions = False):
scene = Scene()
fl = 'Examples/example_files/one_neuron.json'
scene.add_neurons(fl, soma_color='darkseagreen', force_to_hemisphere="right",)
if show_regions:
scene.add_brain_regions(['ZI', 'PAG', 'MRN', 'NPC', "VTA", "STN", "PPT", "SCm", "HY"],
use_original_color=True, alpha=.5)
set_camera(scene)
scene.render()
def CellsScene():
# Load and clean data
data = pd.read_csv('/Users/federicoclaudi/Downloads/41593_2019_354_MOESM3_ESM.csv')
data = data[['genotype', 'Xpos', 'Ypos', 'z.position']]
data.columns = ['genotype', 'x', 'y', 'z']
# Visualise data
scene = Scene()
scene.add_cells(data)
set_camera(scene)
scene.render()
def ConnectivityScene():
scene = Scene()
p0 = scene.get_region_CenterOfMass("ZI")
# Then we se these coordinates to get tractography data, note: any set of X,Y,Z coordinates would do.
tract = aba.get_projection_tracts_to_target(p0=p0)
scene.add_tractography(tract, display_injection_structure=False, color_by="region",
display_injection_volume=True, others_alpha=.25)
scene.add_brain_regions(['ZI'], colors="ivory", alpha=1)
set_camera(scene)
scene.render()
def NeuronsScene3():
scene = Scene()
neurons_metadata = mouselight_fetch_neurons_metadata(filterby='soma', filter_regions=['VAL'])
neurons_files = download_neurons(neurons_metadata[2:6])
scene.add_neurons(neurons_files, soma_color='deepskyblue', force_to_hemisphere="right")
scene.add_brain_regions(['VAL'], use_original_color=False, colors='palegreen', alpha=.9)
mos = scene.actors['regions']['VAL']
scene.edit_actors([mos], wireframe=True)
streamlines_files, data = streamlines_api.download_streamlines_for_region("VAL")
scene.add_streamlines(data[:1], color="palegreen", show_injection_site=False, alpha=.2, radius=10)
set_camera(scene)
scene.render()
def StreamlinesScene2():
scene = Scene()
streamlines_files, data = streamlines_api.download_streamlines_for_region("VAL")
scene.add_streamlines(data, color="palegreen", show_injection_site=False, alpha=.3, radius=10)
streamlines_files, data = streamlines_api.download_streamlines_for_region("VM")
scene.add_streamlines(data, color="palevioletred", show_injection_site=False, alpha=.3, radius=10)
scene.add_brain_regions(['VAL'], use_original_color=False, colors='palegreen', alpha=.9, hemisphere='right')
mos = scene.actors['regions']['VAL']
scene.edit_actors([mos], wireframe=True)
scene.add_brain_regions(['VM'], use_original_color=False, colors='palevioletred', alpha=.9, hemisphere='right')
mos = scene.actors['regions']['VM']
scene.edit_actors([mos], wireframe=True)
set_camera(scene)
scene.render()
from BrainRender.Utils.MouseLightAPI.mouselight_download_neurons import *
from BrainRender.Utils.videomaker import VideoMaker
except:
raise ValueError("Failed at imports")
import os
from random import choice
import pandas as pd
import numpy as np
import random
import json
# ! TESTING SCENE CREATION
print("Ceating scene + adding brain rgions")
try:
scene = Scene()
regions = ["MOs", "VISp", "ZI"]
scene.add_brain_regions(regions, colors="green")
except:
raise ValueError("Failed at SCENE")
# ! TESTING NEURONS RENDERING
print("Rendering neurons")
try:
neurons_metadata = mouselight_fetch_neurons_metadata(
filterby='soma', filter_regions=['MOs'])
neurons_files = download_neurons(neurons_metadata[:2])
parser = NeuronsParser(scene=scene,
color_neurites=True,