Command Line Interface - BlueBrain/NeuroMorphoVis GitHub Wiki
NeuroMorphoVis can be executed in the background mode from the command line usign the neuromorphovis.py script.
Options
The full list of the command line options is shown below.
$ ./neuromorphovis.py -h
usage: neuromorphovis.py [-h] [--blender BLENDER] [--input INPUT]
[--morphology-file MORPHOLOGY_FILE]
[--morphology-directory MORPHOLOGY_DIRECTORY]
[--gid GID] [--target TARGET]
[--blue-config BLUE_CONFIG]
[--output-directory OUTPUT_DIRECTORY]
[--soma-stiffness SOMA_STIFFNESS]
[--soma-subdivision-level SOMA_SUBDIVISION_LEVEL]
[--reconstruct-morphology-skeleton]
[--morphology-reconstruction-algorithm MORPHOLOGY_RECONSTRUCTION_ALGORITHM]
[--morphology-skeleton MORPHOLOGY_SKELETON]
[--soma-representation SOMA_REPRESENTATION]
[--ignore-axon] [--ignore-basal-dendrites]
[--ignore-apical-dendrites]
[--axon-branching-order AXON_BRANCHING_ORDER]
[--apical-dendrites-branching-order APICAL_DENDRITES_BRANCHING_ORDER]
[--basal-dendrites-branching-order BASAL_DENDRITES_BRANCHING_ORDER]
[--sections-radii SECTIONS_RADII]
[--radii-scale-factor RADII_SCALE_FACTOR]
[--fixed-section-radius FIXED_SECTION_RADIUS]
[--bevel-sides BEVEL_SIDES] [--spines SPINES]
[--spines-quality SPINES_QUALITY]
[--random-spines-percentage RANDOM_SPINES_PERCENTAGE]
[--add-nucleus] [--soma-color SOMA_COLOR]
[--axon-color AXON_COLOR]
[--basal-dendrites-color BASAL_DENDRITES_COLOR]
[--apical-dendrites-color APICAL_DENDRITES_COLOR]
[--spines-color SPINES_COLOR]
[--nucleus-color NUCLEUS_COLOR]
[--articulation-color ARTICULATION_COLOR]
[--shader SHADER] [--reconstruct-soma-mesh]
[--reconstruct-neuron-mesh]
[--meshing-algorithm MESHING_ALGORITHM]
[--edges EDGES] [--surface SURFACE]
[--branching BRANCHING]
[--tessellation-level TESSELLATION_LEVEL]
[--global-coordinates] [--export-morphology-swc]
[--export-morphology-h5] [--export-morphology-blend]
[--export-neuron-mesh-ply] [--export-neuron-mesh-obj]
[--export-neuron-mesh-stl]
[--export-neuron-mesh-blend] [--export-soma-mesh-ply]
[--export-soma-mesh-obj] [--export-soma-mesh-stl]
[--export-soma-mesh-blend]
[--render-neuron-morphology]
[--render-neuron-morphology-360]
[--render-neuron-morphology-progressive]
[--render-soma-skeleton] [--render-soma-mesh]
[--render-soma-mesh-360]
[--render-soma-mesh-progressive]
[--render-neuron-mesh] [--render-neuron-mesh-360]
[--render-to-scale] [--rendering-view RENDERING_VIEW]
[--camera-view CAMERA_VIEW]
[--close-up-dimensions CLOSE_UP_DIMENSIONS]
[--full-view-resolution FULL_VIEW_RESOLUTION]
[--close-up-resolution CLOSE_UP_RESOLUTION]
[--resolution-scale-factor RESOLUTION_SCALE_FACTOR]
[--execution-node EXECUTION_NODE]
[--number-cores NUMBER_CORES]
[--job-granularity JOB_GRANULARITY]
[--analyze-morphology]
NeuroMorphoVis: a collaborative framework for analysis and visualization of
morphological skeletons reconstructed from microscopy stacks
optional arguments:
-h, --help show this help message and exit
Blender:
Blender
--blender BLENDER Blender executable
Default: blender, system installed: sudo apt-get install blender
Input:
Input
--input INPUT Input morphology sources.
Options: ['gid', 'target', 'file', 'directory']
--morphology-file MORPHOLOGY_FILE
Morphology file (.H5 or .SWC)
--morphology-directory MORPHOLOGY_DIRECTORY
Morphology directory containing (.H5 or .SWC) files
--gid GID Cell GID (requires BBP circuit).
--target TARGET Cell target in target file (requires BBP circuit).
--blue-config BLUE_CONFIG
BBP circuit configuration
Output:
Output
--output-directory OUTPUT_DIRECTORY
Root output directory
Soma:
Soma
--soma-stiffness SOMA_STIFFNESS
Soma surface stiffness (0.001 - 0.999).
Default 0.25.
--soma-subdivision-level SOMA_SUBDIVISION_LEVEL
Soma surface subdivision level, between (3-7).
Default 5.
Morphology Skeleton:
Morphology Skeleton
--reconstruct-morphology-skeleton
Reconstruct morphology skeleton for visualization or analysis.
--morphology-reconstruction-algorithm MORPHOLOGY_RECONSTRUCTION_ALGORITHM
Morphology reconstruction algorithm.
Options: ['connected-sections',
'(connected-sections-repaired)',
'disconnected-sections',
'disconnected-segments',
'articulated-sections']
--morphology-skeleton MORPHOLOGY_SKELETON
Morphology skeleton style.
Options: ['(original)', 'tapered', 'zigzag', 'tapered-zigzag']
--soma-representation SOMA_REPRESENTATION
Soma representation in the reconstructed morphology.
Options ['ignore', 'sphere', '(profile)']
--ignore-axon Ignore reconstructing the axon.
--ignore-basal-dendrites
Ignore reconstructing basal dendrites.
--ignore-apical-dendrites
Ignore reconstructing apical dendrites.
--axon-branching-order AXON_BRANCHING_ORDER
Maximum branching order for the axon (1, infinity).
Default 5.
--apical-dendrites-branching-order APICAL_DENDRITES_BRANCHING_ORDER
Maximum branching order for the basal dendrites (1, infinity).
Default infinity.
--basal-dendrites-branching-order BASAL_DENDRITES_BRANCHING_ORDER
Maximum branching order for the apical dendrite (1, infinity).
Default infinity.
--sections-radii SECTIONS_RADII
The radii of the morphological sections.
Options: ['(default)', 'scaled', 'fixed']
--radii-scale-factor RADII_SCALE_FACTOR
A scale factor used to scale the radii of the morphology.
Valid only if --sections-radii = scaled.
Default is 1.0
--fixed-section-radius FIXED_SECTION_RADIUS
A fixed radius for all morphology sections.
Valid only if --sections-radii = fixed.
Default is 1.0
--bevel-sides BEVEL_SIDES
Number of sides of the bevel object used to reconstruct the morphology.
Default 16 (4: low quality - 64: high quality)
Spines - Nucleus:
Spines - Nucleus
--spines SPINES Build the spines and integrate them with the mesh.
Options: ['(ignore)', 'circuit', 'random']
--spines-quality SPINES_QUALITY
The quality of the spine meshes.
Options: ['(lq)', 'hq']
--random-spines-percentage RANDOM_SPINES_PERCENTAGE
The percentage of the spines that are added randomly (0-100).
Default 50.
--add-nucleus Add nucleus mesh.
Materials - Colors:
Materials - Colors
--soma-color SOMA_COLOR
Soma color
--axon-color AXON_COLOR
Axon color
--basal-dendrites-color BASAL_DENDRITES_COLOR
Basal dendrites color
--apical-dendrites-color APICAL_DENDRITES_COLOR
Apical dendrite color
--spines-color SPINES_COLOR
Spines color
--nucleus-color NUCLEUS_COLOR
Nucleus color
--articulation-color ARTICULATION_COLOR
Articulations color.
Valid only for the articulated-sections.
Default Yellow.
--shader SHADER Shading mode or material.
Options: (lambert)
electron-light
electron-dark
super-electron-light
super-electron-dark
shadow
flat
subsurface-scattering
Meshing:
Meshing
--reconstruct-soma-mesh
Reconstruct the mesh of the soma only.
--reconstruct-neuron-mesh
Reconstruct the mesh of the entire neuron.
--meshing-algorithm MESHING_ALGORITHM
Meshing algorithm.
Options: ['(piecewise-watertight)', 'union', 'bridging']
--edges EDGES Arbors edges.
This option only applies to the meshes.
Options: ['smooth', '(hard)']
--surface SURFACE The surface roughness of the neuron mesh.
Options: ['rough', '(smooth)']
--branching BRANCHING
Arbors branching based on angles or radii.
Options : ['angles', '(radii)']
--tessellation-level TESSELLATION_LEVEL
Mesh tessellation factor between (0.1, 1.0).
Default 1.0.
--global-coordinates Export the mesh at global coordinates.
Valid only for BBP circuits.
Export Options:
You can export morphology skeletons or reconstructed meshes in various
file formats.
--export-morphology-swc
Exports the morphology to (.SWC) file.
--export-morphology-h5
Exports the morphology to (.H5) file.
--export-morphology-blend
Exports the morphology as a Blender file (.BLEND).
--export-neuron-mesh-ply
Exports the neuron mesh to (.PLY) file.
--export-neuron-mesh-obj
Exports the neuron mesh to (.OBJ) file.
--export-neuron-mesh-stl
Exports the neuron mesh to (.STL) file.
--export-neuron-mesh-blend
Exports the neuron mesh as a Blender file (.BLEND).
--export-soma-mesh-ply
Exports the soma mesh to a (.PLY) file.
--export-soma-mesh-obj
Exports the soma mesh to a (.OBJ) file.
--export-soma-mesh-stl
Exports the soma mesh to a (.STL) file.
--export-soma-mesh-blend
Exports the soma mesh to a Blender file (.BLEND).
Rendering:
Rendering
--render-neuron-morphology
Render image of the morphology skeleton.
--render-neuron-morphology-360
Render a 360 sequence of the morphology skeleton.
--render-neuron-morphology-progressive
Render a progressive reconstruction of the morphology skeleton.
--render-soma-skeleton
Render a static image of the soma skeleton (connected profile).
--render-soma-mesh Render an image of the reconstructed soma mesh.
--render-soma-mesh-360
Render a 360 sequence of the reconstructed soma mesh.
--render-soma-mesh-progressive
Render a sequence of the progressive reconstruction of the soma mesh.
--render-neuron-mesh Render an image of the reconstructed neuron mesh.
--render-neuron-mesh-360
Render a 360 sequence of the reconstructed neuron mesh.
--render-to-scale Render the skeleton to scale.
--rendering-view RENDERING_VIEW
The rendering view of the skeleton for the skeleton.
Options: ['close-up', 'mid-shot', '(wide-shot)']
--camera-view CAMERA_VIEW
The camera direction.
Options: ['(front)', 'side', 'top']
--close-up-dimensions CLOSE_UP_DIMENSIONS
Close up dimensions (the view around the soma in microns).
Valid only when the --rendering-view = close-up.
Default 20.
--full-view-resolution FULL_VIEW_RESOLUTION
Base resolution of full view images (wide-shot or mid-shot).
Default 1024.
--close-up-resolution CLOSE_UP_RESOLUTION
Base resolution of close-up images.
Valid only when the --rendering-view = close-up.
Default 512.
--resolution-scale-factor RESOLUTION_SCALE_FACTOR
A factor used to scale the resolution of the image.
Valid only if --render--to-scale is set.
Default 1.
Execution:
Execution
--execution-node EXECUTION_NODE
Execution is local or using cluster nodes.
Options: ['(local)', 'cluster']
--number-cores NUMBER_CORES
Number of execution cores on cluster.
Default 256.
--job-granularity JOB_GRANULARITY
The granularity of the jobs running on the cluster.
Options: ['high', '(low)']
Analysis:
Analysis
--analyze-morphology Analyze the morphology skeleton and report the artifacts.
Basic Command
To run NeuroMorphoVis on a single morphology that is specified by a GID in a circuit, the user must set the --input option to gid and specify the circuit by a circuit configuration file using the option --blue-config.
neuromorphovis.py \
--input=gid --blue-config=BLUE_CONFIG_FILE --gid=NEURON_GID \
--output=OUTPUT_DIRECTORY
NeuroMoprhoVis can be used to process multiple morphology files grouped in a cell target if the user sets the --input to target and then specifies the target in the --target option.
neuromorphovis.py \
--input=target --blue-config=BLUE_CONFIG_FILE --target=CELL_TARGET \
--output=OUTPUT_DIRECTORY
neuromorphovis.py \
--input=file --morphology-file=MORPHOLOGY_FILE \
--output=OUTPUT_DIRECTORY
neuromorphovis.py \
--input=directory --morphology-directory=MORPHOLOGY_DIRECTORY \
--output=OUTPUT_DIRECTORY
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