CLI
VessMorphoVis can be executed in the background mode from the command line using the vessmorphovis.py script.
The full list of the command line options is shown below.
$ ./vessmorphovis.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
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']
--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)
Materials - Colors:
Materials - Colors
--color COLOR Material color
--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-mesh-ply
Exports the vascular mesh to (.PLY) file.
--export-mesh-obj
Exports the vascular mesh to (.OBJ) file.
--export-mesh-stl
Exports the vascular mesh to (.STL) file.
--export-mesh-blend
Exports the vascular mesh as a Blender file (.BLEND).
Rendering:
Rendering
--render-morphology
Render image of the morphology skeleton.
--render--morphology-360
Render a 360 sequence of the morphology skeleton.
--render-morphology-progressive
Render a progressive reconstruction of the morphology skeleton.
--render-mesh Render an image of the reconstructed vascular mesh.
--render-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
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