Vesuvius Volume Browser

A simple browser built with Rust and egui to browse volume data from the Vesuvius Challenge data set.

It does not require to download any data upfront.

All the published volumes published so far are supported:

• Scroll 1
• Scroll 2
• Scroll 0332
• Scroll 1667
• Scroll 172
• Fragments 1 - 4 (from the Kaggle competition)
• Fragment PHerc0051Cr04Fr08
• Fragment PHerc1667Cr01Fr03

Known surface segments are shown in the catalog and can be rendered on a 4th pane.

Features

• Access to the full volume data set, data is converted to a more efficient format by a background server
• A catalog of known surface segments will allow on-the-fly downloading of surfaces meshes and live rendering
• Rendering options for volumes:
  • thresholding
  • bit depth reduction
  • showing different bit planes
• Rendering options for surfaces:
  • trilinear interpolation
  • show surface outline on the volume panes
  • show xyz outline on the surface pane
  • synchronized panning and zooming between the panes

Installation

Grab a binary from the latest release.

Usage

Install required X11 libraries:

• Ubuntu: apt install -y libgl1 libxrandr2 libxi6 libxcursor1
• MacOSX: Should work out of the box
• Windows: Should work out of the box

Simple browsing:

./vesuvius-gui

When run without any arguments, the app will download the volume data from the tiles server and cache them in a local directory (below the OS-specific cache directory).

Specifying options:

Use the --help flag to see all available options:

Vesuvius GUI, an app to visualize and explore 3D data of the Vesuvius Challenge (https://scrollprize.org)

Usage: vesuvius-gui [OPTIONS]

Options:
  -d, --data-directory <DATA_DIRECTORY>
          Override the data directory. By default, a directory in the user's cache is used
      --obj <OBJ>
          Browse segment from obj file. You need to also provide --width and --height. Provide the --volume if the segment does not target Scroll 1a / 20230205180739
      --width <WIDTH>
          Width of the segment file when browsing obj files
      --height <HEIGHT>
          Height of the segment file when browsing obj files
  -o, --overlay <OVERLAY>
          A directory that contains data to overlay. Only zarr arrays are currently supported
  -v, --volume [<VOLUME>]
          The id of a volume to open
  -h, --help
          Print help

vesuvius-render

vesuvius-render is a tool to render .obj files of segments to layer files similar to VC and scroll-renderer with a self-contained < 5 MB binary.

Features:

• CPU-based multi-threaded rendering
• Input data: vesuvius-tiles based data blocks (for now) automatically downloaded during the process
• Output formats: tiff, png, jpeg

Synopsis:

Vesuvius Renderer, a tool to render segments from obj files

Usage: vesuvius-render [OPTIONS] --obj <OBJ> --width <WIDTH> --height <HEIGHT> --target-dir <TARGET_DIR>

Options:
      --obj <OBJ>
          Provide segment file to render
      --width <WIDTH>
          Width of the segment file when browsing obj files
      --height <HEIGHT>
          Height of the segment file when browsing obj files
      --target-dir <TARGET_DIR>
          The target directory to save the rendered images
      --middle-layer <MIDDLE_LAYER>
          Output layer id that corresponds to the segment surface (default 32)
      --min-layer <MIN_LAYER>
          Minimum layer id to render (default 25)
      --max-layer <MAX_LAYER>
          Maximum layer id to render (default 41)
      --crop <CROP>
          Crop a specific region from the segment. The format is <left>+<top>-<width>x<height>
      --target-format <TARGET_FORMAT>
          File extension / image format to use for layers (default png)
  -v, --volume <VOLUME>
          The id of a volume to render against, otherwise Scroll 1A is used
  -d, --data-directory <DATA_DIRECTORY>
          Override the data directory. By default, a directory in the user's cache is used
      --tile-size <TILE_SIZE>
          The tile size to split a segment into (for ergonomic reasons) (default 1024)
      --concurrent-downloads <CONCURRENT_DOWNLOADS>
          The number of concurrent downloads to use (default 64)
      --retries <RETRIES>
          The number of retries to use for downloads (default 20)
      --stream-buffer-size <STREAM_BUFFER_SIZE>
          Internal stream buffer size (default 1024) This limits the amount of internal work to buffer before backpressuring and continue working on output
      --worker-threads <WORKER_THREADS>
          CPU-bound worker threads to use (default number of cores/threads)
  -h, --help
          Print help

Demo:

Data License

Accessing the data on https://vesuvius.virtual-void.net/ or through this app requires you to fill out the official form and agree to the terms of the data license. See https://scrollprize.org/data.

License

Code released under the MPL 2.0. See LICENSE for the full license text.