cellshape-helper 0.0.13rc0

3D shape analysis using deep learning

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Cellshape-helper provides the ability to convert 3D masks to point clouds.

To install

Step 1: Install PyMesh:

This package relies on PyMesh which needs to be installed first. To install, check out the source code from GitHub:

• Clone the PyMesh repo into a directory of your choice:

git clone https://github.com/PyMesh/PyMesh.git
cd PyMesh
git submodule update --init
export PYMESH_PATH=`pwd`

• On Linux, the system dependencies can be installed with apt-get:

apt-get install \
   libeigen3-dev \
   libgmp-dev \
   libgmpxx4ldbl \
   libmpfr-dev \
   libboost-dev \
   libboost-thread-dev \
   libtbb-dev \
   python3-dev

• On MacOS, the system dependencies can be installed with MacPorts:

port install
    python36 \
    eigen3 \
    gmp \
    mpfr \
    tbb \
    boost

• Python dependencies such as NumPy and SciPy can be installed using pip:

pip install -r $PYMESH_PATH/python/requirements.txt

• Build PyMesh with setuptools:

./setup.py build

• Install PyMesh:

./setup.py install  # May require root privilege

• Alternatively, one can install PyMesh locally:

./setup.py install --user

• Check if PyMesh was installed correctly:

python -c "import pymesh; pymesh.test()"

• Please refer to the PyMesh installation guide if there are any issues.

Step 2: Install cellshape-helper

pip install cellshape-helper

Usage

import cellshape_helper as helper


PATH_TO_TIF_FILES = "path/to/tif/files/"
PATH_TO_SAVE_MESH = "path/to/save/mesh/files/"
PATH_TO_SAVE_PC = "path/to/save/pointcloud/files/"
NUM_POINTS = 2048

helper.tif_to_pc_directory(PATH_TO_TIF_FILES, 
                           PATH_TO_SAVE_MESH, 
                           PATH_TO_SAVE_PC, 
                           NUM_POINTS)

Parameters

• PATH_TO_TIF_FILES: str.
  The path to you binary masks of cells or nuclei.
• PATH_TO_SAVE_MESH: str.
  The path where you want to save the mesh objects to.
• PATH_TO_SAVE_PC: str.
  The path where you want to save your point clouds to.
• NUM_POINTS: str.
  The number of points to sample from the mesh object when creating a point cloud.

For developers

• Fork the repository
• Clone your fork

git clone https://github.com/USERNAME/cellshape-helper 

• Install an editable version (-e) with the development requirements (dev)

cd cellshape-voxel
pip install -e .[dev] 

• To install pre-commit hooks to ensure formatting is correct:

pre-commit install

• To release a new version:

Firstly, update the version with bump2version (bump2version patch, bump2version minor or bump2version major). This will increment the package version (to a release candidate - e.g. 0.0.1rc0) and tag the commit. Push this tag to GitHub to run the deployment workflow:

git push --follow-tags

Once the release candidate has been tested, the release version can be created with:

bump2version release