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Installation
============
.. seealso:: What has been changed recently? Check out the :doc:`release_notes`.
PIMS is easy to install on Windows, OSX, or Linux. Its dependencies are:
* `numpy <http://www.numpy.org/>`_
* `slicerator <https://github.com/soft-matter/slicerator/>`_
For basic image reading one of the following is required:
* `scikit-image <http://scikit-image.org/>`_
* `matplotlib <http://matplotlib.org/>`_
For ipython display of images the following are required:
* `Pillow <http://pillow.readthedocs.org/en/latest/>`__
* `jinja2 <http://jinja.pocoo.org/docs/dev/>`__ (for 3D stacks)
Depending on what file formats you want to read, you will also need:
- `ffmpeg <https://www.ffmpeg.org/>`__ and
`PyAV <http://mikeboers.github.io/PyAV/>`__ (video formats such as
AVI, MOV)
- `jpype <http://jpype.readthedocs.org/en/latest/>`__ (interface with
bioformats to support
`many <https://www.openmicroscopy.org/site/support/bio-formats5.1/supported-formats.html>`__
microscopy formats)
- `Pillow <http://pillow.readthedocs.org/en/latest/>`__ (improved TIFF
support)
- `tifffile <http://www.lfd.uci.edu/~gohlke/code/tifffile.py.html>`__
(alterative TIFF support)
- `imageio <https://imageio.github.io/>`__ (a multi-purpose reader package that
reads and writes many formats)
- `moviepy <http://zulko.github.io/moviepy/>`__ (a Python module that supports
video editing)
- `pims\_nd2 <https://github.com/soft-matter/pims_nd2>`__ (improved
Nikon .nd2 support)
Recommended: conda
------------------
.. note::
To get started with Python on any platform, download and install
`Anaconda <https://store.continuum.io/cshop/anaconda/>`_.
It comes with the common scientific Python packages built in.
With `Anaconda <https://store.continuum.io/cshop/anaconda/>`_
(or `Miniconda <http://conda.pydata.org/miniconda.html>`_) installed,
type the following into a Terminal to install PIMS. That's "Terminal" on a Mac,
and "Start > Applications > Command Prompt" on Windows. Type these lines:
.. code-block:: bash
conda install -c conda-forge pims
The above installs the latest stable release. Finally, to try it out, type:
.. code-block:: bash
ipython notebook
Development version
-------------------
To install the version under active development, with the latest tested code,
install directly from github.
.. code-block:: bash
conda install pip
pip install https://github.com/soft-matter/pims/archive/master.zip
pip
---
PIMS can also be installed using pip.
.. code-block:: bash
pip install pims
source
------
If you plan to edit the code, you can install PIMS manually.
.. code-block:: bash
git clone https://github.com/soft-matter/pims
cd pims
python setup.py develop
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