neuralib.atlas.brainrender.probe.ProbeRenderCLI

class neuralib.atlas.brainrender.probe.ProbeRenderCLI

Bases: BrainRenderCLI

Probe track reconstruction with brainrender

__init__()

Methods

__init__()
export(reconstructor[, output, areas, alpha])	Export reconstruction as html
get_atlas_brain_globe([check_latest])
main([args, parse_only, system_exit])	parsing the commandline input args and call run().
new_parser(**kwargs)	create an ArgumentParser.
post_parsing()
render()	brainrender interactive
render_output()	io handling.
run()	called after main().
video_maker(output_file)	generate video

Attributes

DEFAULT_REGION_COLORS
DESCRIPTION	parser description.
EPILOG	parser epilog.
GROUP_OPTIONAL
GROUP_OUTPUT
GROUP_PROBE
GROUP_REGION
GROUP_SETTINGS
USAGE	parser usage.
annotation	whether draw point annotation.
background	background color (default: 'white')
camera_angle	camera angle (default: 'three_quarters')
coordinate_space	which coordinate space, by default ccf (default: 'ccf')
dye_label_only	only show the histology dye parts (default: False)
file	multi-shank npy or csv file to be inferred
hemisphere	which hemisphere for rendering the region (default: 'both')
implant_depth	implant depth in um
logger
no_root	render without root(brain) mesh (default: False)
output	output path for the html, if None, preview (default: None)
plane_type	cutting orientation to infer the multi-shank label point/probe_idx (default: 'coronal')
print_name	print acronym and the corresponding name (default: False)
print_tree	print tree for the available regions for the given source (default: False)
region_colors	region(s) color (default: None)
regions	region(s) name (default: ())
regions_alpha	region alpha value (default: 0.35)
remove_outside_brain	remove reconstruction outside the brain (default: False)
root_alpha	root alpha (default: 0.35)
shader_style	Shader style to use (default: 'plastic')
shank_interval	shank interval in um if multi-shank (default: None)
source	atlas source name.
title	title added to the top of the window (default: None)
tree_init	init region for the tree print (default: None)
video_output	video output path (default: None)
scene

DESCRIPTION: str | None = 'Probe track reconstruction with brainrender'

parser description. Could be override as a method if its content is dynamic-generated.

GROUP_PROBE = 'Probe Option'

implant_depth: int

implant depth in um

shank_interval: int | None

shank interval in um if multi-shank (default: None)

dye_label_only: bool

only show the histology dye parts (default: False)

remove_outside_brain: bool

remove reconstruction outside the brain (default: False)

file: Path

multi-shank npy or csv file to be inferred

plane_type: Literal['coronal', 'sagittal', 'transverse']

cutting orientation to infer the multi-shank label point/probe_idx (default: ‘coronal’)

post_parsing()

run()

called after main(). Used for runs the main execution logic of the object

render()

brainrender interactive