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Expand Up @@ -6,16 +6,16 @@ CT scans of ancient, badly damaged manuscripts, but can be applied in many
volumetric analysis applications.

## Getting started
New to Volume Cartographer? A great place to get started with virtual unwrapping
is the [tutorial](https://scrollprize.org/tutorial3) put together by
[the Vesuvius Challenge](https://scrollprize.org/).
New to Volume Cartographer? A great place to get started with virtual unwrapping
is the [tutorial](https://scrollprize.org/tutorial3) put together by
the [Vesuvius Challenge](https://scrollprize.org/).

You can also browse our [application list](docs/pages/apps-list.md) for an
You can also browse our [application list](docs/pages/apps-list.md) for an
overview of our available applications and utilities.

## Installation
### Using Homebrew
We provide pre-built binaries for our tools through our
We provide pre-built binaries for our tools through our
[Homebrew Casks tap](https://github.com/educelab/homebrew-casks):

```shell
Expand All @@ -27,16 +27,16 @@ Gatekeeper on Apple Silicon devices without explicit approval. Since many of
our tools are run from the command line, we suggest installing with Homebrew's
`--no-quarantine` flag.

The main `VC.app` GUI will be installed to `/Applications/` and the command line
The main `VC.app` GUI will be installed to `/Applications/` and the command line
tools should be immediately available in Terminal:

```shell
vc_render --help
```

### Using Docker
We provide multi-architecture Docker images in the GitHub Container Registry.
Simply pull our container and Docker will select the appropriate image for your
We provide multi-architecture Docker images in the GitHub Container Registry.
Simply pull our container and Docker will select the appropriate image for your
host platform:

```shell
Expand All @@ -58,16 +58,16 @@ Usage:

General Options:
-h [ --help ] Show this message
--cache-memory-limit arg Maximum size of the slice cache in
bytes. Accepts the suffixes:
--cache-memory-limit arg Maximum size of the slice cache in
bytes. Accepts the suffixes:
(K|M|G|T)(B). Default: 50% of the total
system memory.
--log-level arg (=info) Options: off, critical, error, warn,
--log-level arg (=info) Options: off, critical, error, warn,
info, debug
...
```

To run the GUI tools, you must additionally set up
To run the GUI tools, you must additionally set up
[X11 forwarding from the container](docs/pages/running-gui-tools.md).

### From source
Expand Down Expand Up @@ -96,22 +96,22 @@ explicitly support other platforms.
- This project will automatically check if the compiler provides
`std::filesystem`. If it is not found, then Boost Filesystem is required.
This behavior can be controlled with the `VC_USE_BOOSTFS` CMake flag.
* [Doxygen](http://www.doxygen.org/): Required to build
* [Doxygen](https://www.doxygen.nl/): Required to build
documentation.
* [pybind11](https://github.com/pybind/pybind11): Required to build Python
bindings.

##### (macOS) Homebrew-provided dependencies
In principle, Homebrew can be used to install all of Volume Cartographer's
dependencies. However at the time of this writing, the `vtk` brew package links
against Qt5 while the Volume Cartographer GUIs link against Qt6. This will lead
to linking errors when compiling this project. To use the Homebrew version of
VTK, you must disable compilation of the VC GUI apps with the
`-DVC_BUILD_GUI=OFF` CMake flag. Otherwise, you must build VTK from source or
follow the instructions for
[building vc-deps dependencies](#(Optional)-Use-vc-deps-dependencies).

#### Compilation
In principle, Homebrew can be used to install all of Volume Cartographer's
dependencies. However at the time of this writing, the `vtk` brew package links
against Qt5 while the Volume Cartographer GUIs link against Qt6. This will lead
to linking errors when compiling this project. To use the Homebrew version of
VTK, you must disable compilation of the VC GUI apps with the
`-DVC_BUILD_GUI=OFF` CMake flag. Otherwise, you must build VTK from source or
follow the instructions for
[building vc-deps dependencies](#optional-use-vc-deps-dependencies).

#### Compilation
This project is built and installed using the CMake build system. If you have
already installed the dependencies listed above, compilation should be as simple
as:
Expand All @@ -124,9 +124,9 @@ cmake --build build/
```

Many `volume-cartographer` libraries can be built in parallel, and compilation
times will be improved by running `cmake --build build/ -j4`. Alternatively,
you can use CMake to generate [Ninja](https://ninja-build.org/) build system
files:
times will be improved by running `cmake --build build/ -j4`. Alternatively,
you can use CMake to generate [Ninja](https://ninja-build.org/) build system
files:
```shell
cmake -S . -B build/ -GNinja -DCMAKE_BUILD_TYPE=Release
cmake --build build/ # automatically builds in parallel with Ninja
Expand All @@ -142,10 +142,10 @@ cmake --install build/ # --prefix ~/custom/install/prefix/
To assist with installing dependencies, we have created the
[vc-deps project](https://github.com/educelab/vc-deps). While this project can
be used on its own to install volume-cartographer dependencies to the system, it
is also available as a git submodule within `volume-cartographer`. Note that
is also available as a git submodule within `volume-cartographer`. Note that
`vc-deps` **does not** install CMake or Qt.

To build and link against the in-source `vc-deps` libraries, run the following:
To build and link against the in-source `vc-deps` libraries, run the following:
```shell
# Get the source code plus all submodules
git clone --recursive https://github.com/educelab/volume-cartographer.git
Expand Down Expand Up @@ -211,7 +211,7 @@ cmake -S . -B build/ -DVC_BUILD_DOCS=ON -DVC_INSTALL_DOCS=ON

## Python bindings
We currently maintain limited Python binding support through pybind11. They are
a work-in-progress and should not be used in production code.
a work-in-progress and should not be used in production code.

Bindings can be built and installed by setting the
`VC_BUILD_PYTHON_BINDINGS` and `VC_INSTALL_PYTHON_BINDINGS` flags:
Expand Down Expand Up @@ -260,31 +260,31 @@ This project incorporates software from many excellent external libraries and
projects. Please see [NOTICE](NOTICE) for more information about the licensing
terms of these projects.

**Volume Cartographer** and the project logo and banner graphics are trademarks
**Volume Cartographer** and the project logo and banner graphics are trademarks
of EduceLab.

## Citation and references
If you use Volume Cartographer in your research, please cite this repository
in your publication using
[our Zenodo record](https://doi.org/10.5281/zenodo.4604881). For more
information about the concepts of virtual unwrapping, please see the following
If you use Volume Cartographer in your research, please cite this repository
in your publication using
[our Zenodo record](https://doi.org/10.5281/zenodo.4604881). For more
information about the concepts of virtual unwrapping, please see the following
publications:
* William Brent Seales et al. “From damage to discovery via virtual unwrapping:
Reading the scroll from En-Gedi”. In: _Science Advances_ 2.9 (2016).
doi: 10.1126/sciadv.1601247. [[link]](http://advances.sciencemag.org/content/2/9/e1601247)
doi: 10.1126/sciadv.1601247. [[link]](https://www.science.org/doi/10.1126/sciadv.1601247)
* Clifford Seth Parker, William Brent Seales, and Pnina Shor. “Quantitative
Distortion Analysis of Flattening Applied to the Scroll from En-Gedi”. In:
Art & Archaeology, 2nd International Conference. 2016.
Art & Archaeology, 2nd International Conference. 2016.
[[link]](https://arxiv.org/abs/2007.15551)
* W Brent Seales and Daniel Delattre. “Virtual unrolling of carbonized
Herculaneum scrolls: Research Status (2007–2012)”. In: Cronache Ercolanesi 43
* W Brent Seales and Daniel Delattre. “Virtual unrolling of carbonized
Herculaneum scrolls: Research Status (2007–2012)”. In: Cronache Ercolanesi 43
(2013), pp. 191–208.
* Ryan Baumann, Dorothy Carr Porter, and W Brent Seales. “The use of micro-ct
in the study of archaeological artifacts”. In: 9th International Conference
* Ryan Baumann, Dorothy Carr Porter, and W Brent Seales. “The use of micro-ct
in the study of archaeological artifacts”. In: 9th International Conference
on NDT of Art. 2008, pp. 1–9. [[link]](https://www.ndt.net/article/art2008/papers/244Seales.pdf)
* Yun Lin and W Brent Seales. “Opaque document imaging: Building images of
inaccessible texts”. In: Computer Vision, 2005. ICCV 2005. Tenth IEEE
* Yun Lin and W Brent Seales. “Opaque document imaging: Building images of
inaccessible texts”. In: Computer Vision, 2005. ICCV 2005. Tenth IEEE
International Conference on. Vol. 1. IEEE. 2005, pp. 662–669.
* W Brent Seales and Yun Lin. “Digital restoration using volumetric scanning”.
In: Digital Libraries, 2004. Proceedings of the 2004 Joint ACM/IEEE
Conference on. IEEE. 2004, pp. 117–124.
* W Brent Seales and Yun Lin. “Digital restoration using volumetric scanning”.
In: Digital Libraries, 2004. Proceedings of the 2004 Joint ACM/IEEE
Conference on. IEEE. 2004, pp. 117–124.

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