Command Line Interface
NeuroMorphoVis can be executed in the background mode from the command line usign the neuromorphovis.py script.
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.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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