Esempio n. 1
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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() 
Esempio n. 2
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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()
Esempio n. 3
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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()
Esempio n. 4
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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()
Esempio n. 5
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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() 
Esempio n. 6
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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() 
Esempio n. 7
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    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,
Esempio n. 8
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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()
Esempio n. 9
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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()