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Volume Cartographer Apps and Utilities

An exhaustive list of the applicaitons and utilities provided by Volume Cartographer. Most programs can be run with --help for more usage details.

VC

The primary GUI interface for performing segmentation with Volume Cartographer.

Installation note: On macOS, this program is compiled into VC.app and can be run by double-clicking the app bundle. When installing with Homebrew, VC.app is placed in /Applications/. On all other platforms, the VC executable is installed to the system prefix and can be launched from the command line.

CannySegment

A segmentation tool which uses canny edge detection to identify surface points. More details on working with CannySegment are available here.

Installation note: This program is primarily a command line tool, but is compiled into CannySegment.app on macOS because it contains optional GUI components. It can be launched by running the packaged executable:

./CannySegment.app/Contents/MacOS/CannySegment

When installing via Homebrew, the packaged executable is symlinked to $(brew --prefix)/bin/vc_canny_segment and can be run directly. If installing from source, you can create your own symlink into the system search path:

# Installing from source on macOS only
# ln -s ./CannySegment.app/Contents/MacOS/CannySegment /usr/local/bin/vc_canny_segment
vc_canny_segment

MeshProject

Visualization tool that draws the intersection of a mesh/meshes on the slices of a volume.

Installation note: This program is primarily a command line tool, but is compiled into MeshProject.app on macOS because it contains optional GUI components. It can be launched by running the packaged executable:

./MeshProject.app/Contents/MacOS/MeshProject

When installing via Homebrew, the packaged executable is symlinked to $(brew --prefix)/bin/vc_projection and can be run directly. If installing from source, you can create your own symlink into the system search path:

# Installing from source on macOS only
# ln -s ./MeshProject.app/Contents/MacOS/MeshProject /usr/local/bin/vc_projection
vc_projection

vc_packager

Program for creating and adding volumes to a Volume Package (.volpkg) directory. Volume packages can be thought of as a project directory for the Volume Cartographer suite.

# Make a new .volpkg
vc_packager -v my-project.volpkg -s path/to/first-volume/ --material-thickness 600

# Add a volume to an existing .volpkg
vc_packager -v my-project.volpkg -s path/to/second-volume/

vc_volpkg_explorer

Displays the contents of a Volume Package (.volpkg).

$ vc_volpkg_explorer -v my-project.volpkg 

 --- VolumePkg ---
Name: My unwrapping project
Material Thickness: 1000um

 --- Volumes ---
[20230315130124] Campfire Scroll, 560x560x477, 104um/voxel

 --- Segmentations ---
[20230315130225] 20230315130225, associated volume: 20230315130124

 --- Renders ---

vc_render

The primary tool for rendering (meshing + flattening + texturing) a virtually unwrapped result from a segmentation.

# Use vc_volpkg_explorer to get the segmentation ID for -s
vc_render -v my-project.volpkg -s 20230315130225 -o first-result.obj

vc_layers

Similar to vc_render but outputs a flattened surface volume, the portion of the full volume that is immediately adjacent to the segmentation.

vc_layers -v my-project.volpkg -s 20230315130225 -o first-surface-vol/

vc_render_from_ppm, vc_layers_from_ppm

Special versions of vc_render and vc_layers which use a pre-generated per-pixel map (PPM) rather than meshing and flattening a segmentation. Saves time when you want to compare renders generated using different texturing parameters.

# Generate the PPM
vc_render -v my-project.volpkg -s 20230315130225 -o params-1.tif --output-ppm seg-map.ppm

# Reuse the PPM to generate a new texture with different parameters
vc_render_from_ppm -v my-project.volpkg -p seg-map.ppm -o params-2.tif --filter 3

vc_segment

A command line tool for running segmentation algorithms. To get started, start a new segmentation in the main VC GUI, then use this tool to propagate the result to new slices. Includes the Thinned Flood Fill algorithm, which is not yet available in the GUI.

vc_convert_pointset

Convert a Volume Cartographer point cloud file (.vcps) to a mesh file (PLY/OBJ). Does not perform triangulation.

vc_mesher

Triangulate (i.e. mesh) a Volume Cartographer point cloud file (.vcps). The input point cloud should be ordered (i.e. stored as a 2D matrix), the default type created by VC.

vc_retexture_mesh

Given a textured mesh, replace its texture with in an alternate texture image. Useful if you used vc_render_from_ppm to generate a texture that you want to visualize on a 3D mesh.

vc_flatten_mesh

Flattens a triangulated mesh using one of our parameterization algorithms. The input mesh should have a surface boundary, be manifold, and have consistent winding order.

vc_color_map

Apply a color map to an image file, usually a texture image. Useful when looking for content that may be difficult to see in grayscale.

vc_merge_pointset

Merge multiple point cloud (.vcps) files into a single point cloud. Useful when combining multiple segmentations into a single surface.

vc_visualize_graph

The processing done by vc_render is executed by our smgl graph processing library. This utility allows you to visualize the render graph.

# Create a render in the volpkg by rendering a segmentation
# The Render ID is reported on the command line
vc_render -v my-project.volpkg -s 20230315130225
# [volcart] [info] Created new Render graph in VolPkg: 20230316104344

# Save render graph to a graphviz dot file
vc_visualize_graph -v my-project.volpkg -r 20230316104344 -o graph.gv

# Render image with graphviz
dot -Tpng graph.gv > graph.png

vc_area

Calculates the surface area of a segmentation in physical units.

vc_transform_uv

Rotates and/or flips a mesh's UV map and texture image. Useful if text or content in the texture image appears rotated or flipped with respect to the image axes.

vc_transform_mesh

Apply various linear transforms to a mesh. Primarily useful for visualization purposes.

vc_volpkg_upgrade

We occasionally upgrade the Volume Package (.volpkg) file format to support new features. This tool upgrades existing volume packages to the new format.

vc_repair_pointsets

A bug in certain versions of VC resulted in ordered .vcps files where the z-values of points were off by a few slices. This utility repairs these files by assigning new z-indices to all points relative to the z-index of the first row:

row old z new z
0 400 400
1 400 401
2 401 402
... ... ...
9 408 409
10 410 410
11 410 411

The utility can be run from the command line:

# See what will be modified
vc_repair_pointsets -i pointset.vcps --verbose

# Repair the pointset and save the result to a new file
vc_repair_pointsets -i pointset.vcps -o repaired.vcps

# Backup and repair the pointset
cp pointset.vcps pointset.vcps.orig
vc_repair_pointsets -i pointset.vcps -o pointset.vcps

vc_visualize_ppm

This file generates visualizations of the positions and normals saved in PPM files. Files are saved as 32-bit, RGB TIFs:

# Generate surface_maps_normal.tif and surface_maps_pos.tif
vc_visualize_ppm --volpkg my-project.volpkg --ppm surface.ppm -o surface_maps_

Other utilities

These are extra utilities available in the Volume Cartographer build directory when building from source. They are largely developer tools.

vc_add_alignment_markers
vc_cmap_bar
vc_convert_mask
vc_flip_mesh
vc_generate_ppm
vc_image_stats
vc_invert_cloud
vc_metaedit
vc_ppm_to_pointset
vc_project_mesh
vc_seg_to_pointmask
vc_uv2mesh
vc_volume_bump
vc_volume_client
vc_volume_server