neuralib.atlas.brainrender.probe.ProbeRenderCLI

class neuralib.atlas.brainrender.probe.ProbeRenderCLI[source]

Probe track reconstruction with brainrender

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
`camera_angle`	camera angle
`coordinate_space`	which coordinate space, by default ccf
`dye_label_only`	only show the histology dye parts
`file`	multi-shank npy or csv file to be inferred
`hemisphere`	which hemisphere for rendering the region
`implant_depth`	implant depth in um
`logger`
`no_root`	render without root(brain) mesh
`output`	output path for the html, if None, preview
`plane_type`	cutting orientation to infer the multi-shank label point/probe_idx
`print_name`	print acronym and the corresponding name
`print_tree`	print tree for the available regions for the given source
`region_colors`	region(s) color
`regions`	region(s) name
`regions_alpha`	region alpha value
`remove_outside_brain`	remove reconstruction outside the brain
`root_alpha`	root alpha
`shader_style`	Shader style to use
`shank_interval`	shank interval in um if multi-shank
`source`	atlas source name.
`title`	title added to the top of the window
`tree_init`	init region for the tree print
`video_output`	video output path
`scene`

DESCRIPTION: str = 'Probe track reconstruction with brainrender': parser description. Could be override as a method if its content is dynamic-generated.

plane_type: Literal['coronal', 'sagittal', 'transverse']: cutting orientation to infer the multi-shank label point/probe_idx