LibAPR - The Adaptive Particle Representation Library

Library for producing and processing on the Adaptive Particle Representation (APR) (For article see: https://www.nature.com/articles/s41467-018-07390-9).

Labeled Zebrafish nuclei: Gopi Shah, Huisken Lab (MPI-CBG, Dresden and Morgridge Institute for Research, Madison); see also Schmid et al., Nature Communications 2017

Python support

We now provide python wrappers in a separate repository PyLibAPR

In addition to providing wrappers for most of the LibAPR functionality, the Python library contains a number of new features that simplify the generation and handling of the APR. For example:

• Interactive APR conversion
• Interactive APR z-slice viewer
• Interactive APR raycast (maximum intensity projection) viewer
• Interactive lossy compression of particle intensities

Version 2.0 release notes

The library has changed significantly since release 1.1. There are changes to IO and iteration that are not compatible with the older version.

• New (additional) linear access data structure, explicitly storing coordinates in the sparse dimension, similar to Compressed Sparse Row.
• Block-based decomposition of the APR generation pipeline, allowing conversion of very large images.
• Expanded and improved functionality for image processing directly on the APR:
  • APR filtering (spatial convolutions).
  • APRNumerics module, including e.g. gradient computations and Richardson-Lucy deconvolution.
  • CUDA GPU-accelerated convolutions and RL deconvolution (currently only supports dense 3x3x3 and 5x5x5 stencils)

Dependencies

• HDF5 1.8.20 or higher
• OpenMP > 3.0 (optional, but recommended)
• CMake 3.6 or higher
• LibTIFF 4.0 or higher

NB: This update to 2.0 introduces changes to IO and iteration that are not compatable with old versions.

If compiling with APR_DENOISE flag the package also requires:

• Eigen3.

Building

The repository requires submodules, and needs to be cloned recursively:

git clone --recursive https://github.com/AdaptiveParticles/LibAPR.git

CMake build options

Several CMake options can be given to control the build. Use the -D argument to set each desired option. For example, to disable OpenMP, change the cmake calls below to

cmake -DAPR_USE_OPENMP=OFF ..

Building on Linux

On Ubuntu, install the cmake, build-essential, libhdf5-dev and libtiff5-dev packages (on other distributions, refer to the documentation there, the package names will be similar). OpenMP support is provided by the GCC compiler installed as part of the build-essential package.

For denoising support also requires: libeigen3-dev

In the directory of the cloned repository, run

mkdir build
cd build
cmake ..
make

This will create the libapr.so library in the build directory.

Building on OSX

On OSX, install the cmake, hdf5 and libtiff homebrew packages and have the Xcode command line tools installed.

If you want to compile with OpenMP support (Recommended), also install the llvm and libomp package via homebrew as the clang version shipped by Apple currently does not support OpenMP.

In the directory of the cloned repository, run

mkdir build
cd build
cmake ..
make

Building on Windows

On windows there are two working strategies we have tested. Either cheating and using WSL2 and linux above, or utilising a recent version clang-cl or clang directly as included in MSVC 2019 >16.8.6. Note for earlier versions OpenMP support did not work.

The easiest way to set up your windows environment we have found is using chocolatey + vcpkg.

Chocolatey Install:

First install chocolatey using powershell: https://chocolatey.org/install

Open an admin powershell (for chocolatey steps)

If not installed, install git and cmake:

choco install -y git 
choco install -y cmake.portable

install the required visual studio compiler tools and clang: (Note you can also do this via downloading 2019 community and selecting the correct packages)

choco install visualstudio2019buildtools --params "--add Microsoft.Component.MSBuild --add Microsoft.VisualStudio.Component.VC.Llvm.Clang --add Microsoft.VisualStudio.Component.VC.Llvm.ClangToolset --add Microsoft.VisualStudio.ComponentGroup.NativeDesktop.Llvm.Clang --add Microsoft.VisualStudio.Component.Windows10SDK.19041	--add Microsoft.VisualStudio.Component.VC.Tools.x86.x64 --add Microsoft.VisualStudio.ComponentGroup.UWP.VC.BuildTools"
choco install -y llvm

Now install your dependencies using vcpkg, in an install directory (VCPKG_PATH) of your choice do the following:

git clone https://github.com/microsoft/vcpkg
cd vcpkg
./bootstrap-vcpkg.bat
./vcpkg.exe install blosc:x64-windows gtest:x64-windows tiff:x64-windows hdf5:x64-windows szip:x64-windows

Now navigate to your cloned LibAPR directory (git clone --recursive https://github.com/AdaptiveParticles/LibAPR.git). You should have all dependencies set up to be able to build the library with clang-cl -A x64 -T ClangCL and to search for dependencies from vcpkg at your vcpkg install location: -DCMAKE_TOOLCHAIN_FILE="VCPKG_PATH/vcpkg/scripts/buildsystems/vcpkg.cmake" -DVCPKG_TARGET_TRIPLET=x64-windows .

Now for example to build the tests and examples (Please note you will need to update below with your own VCPKG_PATH from the steps above.

mkdir build
cd build

Cmake -A x64 -DCMAKE_TOOLCHAIN_FILE="VCPKG_PATH/vcpkg/scripts/buildsystems/vcpkg.cmake" -DVCPKG_TARGET_TRIPLET=x64-windows -T ClangCL -DAPR_BUILD_EXAMPLES=ON -DAPR_TESTS=ON ..
cmake --build . --config Release

The above examples is also used in CI and can be executed in the cmake-build_windows.sh

Docker build

We provide a working Dockerfile that installs the library within the image in a separate repository.

Note: not recently tested.

Install instructions

Please see: INSTALL_INSTRUCTIONS.md and https://github.com/AdaptiveParticles/APR_cpp_project_example for a minimal project using the APR.

Examples and Documentation

There are 12 basic examples, that show how to generate and compute with the APR. These can be built by adding -DAPR_BUILD_EXAMPLES=ON to the cmake command.

All examples except Example_get_apr and Example_get_apr_by_block require an already produced APR, such as those created by Example_get_apr*.

For tutorial on how to use the examples, and explanation of data-structures see the library guide.

LibAPR Tests

The testing framework can be turned on by adding -DAPR_TESTS=ON to the cmake command. All tests can then be run by executing

ctest

on the command line in your build folder. Please let us know by creating an issue, if any of these tests are failing on your machine.

Java wrappers

Basic Java wrappers can be found at LibAPR-java-wrapper Not compatable with recent releases.

Coming soon

• Improved documentation and updated library guide.
• More examples of APR-based image processing and segmentation.
• CUDA GPU-accelerated APR generation and additional processing options.
• Time series support.

Contact us

If anything is not working as you think it should, or would like it to, please get in touch with us!! Further, dont hesitate to contact us if you have a project or algorithm you would like to try using the APR for. We would be glad to help!

Citing this work

If you use this library in an academic context, please cite the following paper:

• Cheeseman, Günther, Gonciarz, Susik, Sbalzarini: Adaptive Particle Representation of Fluorescence Microscopy Images (Nature Communications, 2018) https://doi.org/10.1038/s41467-018-07390-9