Metadata-Version: 1.1
Name: ashlar
Version: 1.0.1
Summary: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
Home-page: https://github.com/sorgerlab/ashlar
Author: Jeremy Muhlich
Author-email: jeremy_muhlich@hms.harvard.edu
License: MIT License
Download-URL: https://github.com/sorgerlab/ashlar/archive/v1.0.1.tar.gz
Description-Content-Type: UNKNOWN
Description: # ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
        
        ## Installation (Linux)
        
        ASHLAR is written in Python, but has python dependencies which make use of C.
        
        The recommended way to install ASHLAR is to make use of a fairly comprehensive
        distribution of python binaries called miniconda.
        
        Note: Users with an existing python environment may wish to skip the final step
        adding the conda bin directory to the `PATH` as this will override the current
        for all shells. Instead, the `PATH` can be added as and when needed.
        
        ```bash
        # Define an installation directory, e.g.
        export CONDA_ROOT=/opt/ashlarconda
        
        # Download Minconda (Python 2) installer
        wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
        
        # Run miniconda installer
        sh Miniconda2-latest-Linux-x86_64.sh -b -u -p ${CONDA_ROOT}
        
        # Install conda packages required
        ${CONDA_ROOT}/bin/conda install -q -y numpy matplotlib networkx pathlib2 \
            scipy scikit-image scikit-learn
        
        # Install conda packages from other channels required
        ${CONDA_ROOT}/bin/conda install -q -y -c conda-forge pyfftw
        
        # Install pip packages required (not available or up-to-date in conda)
        ${CONDA_ROOT}/bin/pip install -q -U ModestImage javabridge python-bioformats
        
        # Install ASHLAR
        ${CONDA_ROOT}/bin/pip install -q -U \
            git+https://github.com/dpwrussell/ashlar@module
        
        # Make this conda install available on your PATH
        echo ${CONDA_ROOT}/bin':$PATH' >> ~/.bashrc
        ```
        
        ## Installation (Windows)
        
        TBD
        
        ## Usage
        
        ```bash
        mosaic <scan_path> [--ffc <flat_field_path>]
        ```
        
Keywords: scripts,microscopy,registration,stitching
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: End Users/Desktop
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 2
Classifier: Topic :: Scientific/Engineering :: Visualization
