sorgerlab/ashlar

Name: ashlar

Owner: sorgerlab

Description: ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration

Created: 2017-05-15 11:19:52.0

Updated: 2017-11-02 20:02:09.0

Pushed: 2017-12-04 04:27:50.0

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Size: 97

Language: Python

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README

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.

fine an installation directory, e.g.
rt CONDA_ROOT=/opt/ashlarconda

wnload Minconda (Python 2) installer
 https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh

n miniconda installer
iniconda2-latest-Linux-x86_64.sh -b -u -p ${CONDA_ROOT}

stall conda packages required
NDA_ROOT}/bin/conda install -q -y numpy matplotlib networkx pathlib2 \
scipy scikit-image scikit-learn

stall conda packages from other channels required
NDA_ROOT}/bin/conda install -q -y -c conda-forge pyfftw

stall pip packages required (not available or up-to-date in conda)
NDA_ROOT}/bin/pip install -q -U ModestImage javabridge python-bioformats

stall ASHLAR
NDA_ROOT}/bin/pip install -q -U \
git+https://github.com/dpwrussell/ashlar@module

ke this conda install available on your PATH
 ${CONDA_ROOT}/bin':$PATH' >> ~/.bashrc

Installation (Windows)

TBD

Usage

ic <scan_path> [--ffc <flat_field_path>]