Metadata-Version: 1.0
Name: PIMS
Version: 0.5rc1
Summary: Python Image Sequence
Home-page: https://github.com/soft-matter/pims
Author: PIMS Contributors
Author-email: dallan@pha.jhu.edu
License: BSD-3-clause
Description: pims: Python Image Sequence
        ===========================
        
        |build status|
        
        What Problem Does PIMS Solve?
        -----------------------------
        
        Scientific video can be packaged in various ways: familiar video formats
        like .AVI and .MOV, folders full of numbered images, or “stacks” of TIFF
        images. Each of these requires a separate Python module. And, once
        loaded, they have different methods for **accessing individual images,
        looping through the images in bulk, accessing a specific range, or
        dealing with multidimensional files**. PIMS can do all of these using a
        consistent interface, handling the differences between different inputs
        invisibly.
        
        Formats readable by pims include: \* Directories or zipfiles of still
        images (most formats, including TIFF, JPEG, PNG, BMP), and TIFF stacks
        \* Microscope images supported by the `Bio-formats
        project <https://www.openmicroscopy.org/site/support/bio-formats5.1/supported-formats.html>`__,
        including Leica, Nikon, Olympus, and Zeiss formats. Requires separate
        installation; see below. \* Movie formats and codecs supported by
        ffmpeg, including AVI, QuickTime MOV, and H.264 (MP4). May require
        separate installation; see below. \* CINE files from Vision Research
        cameras \* SEQ files from NorPix StreamPix software
        
        PIMS is based on readers by: \*
        `scikit-image <http://scikit-image.org/>`__ \*
        `matplotlib <http://matplotlib.org/>`__ \*
        `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 Bio-formats) \*
        `Pillow <http://pillow.readthedocs.org/en/latest/>`__ (improved TIFF
        support) \* `libtiff <https://code.google.com/p/pylibtiff/>`__
        (alternative TIFF support) \*
        `tifffile <https://pypi.org/project/tifffile/>`__ (alterative TIFF
        support) \* `pims_nd2 <https://github.com/soft-matter/pims_nd2>`__
        (improved Nikon .nd2 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) \*
        `nd2reader <https://github.com/rbnvrw/nd2reader>`__ (a Pure Python
        module for reading Nikon NIS Elements ND2 images and metadata)
        
        Examples & Documentation
        ------------------------
        
        Everything is demonstrated in `this IPython
        notebook <http://nbviewer.ipython.org/github/soft-matter/pims/blob/master/examples/loading%20video%20frames.ipynb>`__.
        
        `Read the documentation <http://soft-matter.github.io/pims/>`__ for
        installation instructions, examples, and further reference.
        
        Core Contributors
        -----------------
        
        -  **Daniel Allan** founding contributor, slicing and iteration logic,
           basic readers, display tools
        -  **Thomas Caswell** major refactor, abstract base class
        -  **Casper van der Wel** bioformats readers, display tools
        -  **Thomas Dimiduk** filetype-detecting dispatch logic
        
        Support
        -------
        
        This package was developed in part by Daniel Allan, as part of his PhD
        thesis work on microrheology in Robert L. Leheny’s group at Johns
        Hopkins University in Baltimore, MD. The work was supported by the
        National Science Foundation under grant number CBET-1033985. Later work
        was supported by Brookhaven National Lab. Dan can be reached at
        dallan@bnl.gov.
        
        This package was developed in part by Thomas A Caswell as part of his
        PhD thesis work in Sidney R Nagel’s and Margaret L Gardel’s groups at
        the University of Chicago, Chicago IL. This work was supported in part
        by NSF Grant DMR-1105145 and NSF-MRSEC DMR-0820054. Later work was
        supported by Brookhaven National Lab. Tom can be reached at
        tcaswell@gmail.com.
        
        This package was developed in part by Casper van der Wel, as part of his
        PhD thesis work in Daniela Kraft’s group at the Huygens-Kamerlingh-Onnes
        laboratory, Institute of Physics, Leiden University, The Netherlands.
        This work was supported by the Netherlands Organisation for Scientific
        Research (NWO/OCW).
        
        .. |build status| image:: https://travis-ci.org/soft-matter/pims.png?branch=master
           :target: https://travis-ci.org/soft-matter/pims
        
Platform: UNKNOWN
