Installation

See also

What has been changed recently? Check out the Release notes.

PIMS is easy to install on Windows, OSX, or Linux. Its dependencies are:

• numpy
• slicerator

For basic image reading one of the following is required:

• scikit-image
• matplotlib
• scipy

For ipython display of images the following are required:

• Pillow
• jinja2 (for 3D stacks)

Depending on what file formats you want to read, you will also need:

• ffmpeg and PyAV (video formats such as AVI, MOV)
• jpype (interface with bioformats to support many microscopy formats)
• Pillow (improved TIFF support)
• libtiff (alternative TIFF support)
• tifffile (alterative TIFF support)
• imageio (a multi-purpose reader package that reads and writes many formats)
• moviepy (a Python module that supports video editing)
• pims_nd2 (improved Nikon .nd2 support)

Recommended: conda

Note

To get started with Python on any platform, download and install Anaconda. It comes with the common scientific Python packages built in.

With Anaconda (or Miniconda) 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:

conda install -c conda-forge pims

The above installs the latest stable release. Finally, to try it out, type:

ipython notebook

Development version

To install the version under active development, with the latest tested code, install directly from github.

conda install pip
pip install https://github.com/soft-matter/pims/archive/master.zip

pip

PIMS can also be installed using pip.

pip install pims

source

If you plan to edit the code, you can install PIMS manually.

git clone https://github.com/soft-matter/pims
cd pims
python setup.py develop