Metadata-Version: 1.0
Name: PIMS
Version: 0.3.3
Summary: Python Image Sequence
Home-page: https://github.com/soft-matter/pims
Author: PIMS Contributors
Author-email: dallan@pha.jhu.edu
License: UNKNOWN
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/>`__ \*

        `scipy <http://www.scipy.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 <http://www.lfd.uci.edu/~gohlke/code/tifffile.py.html>`__

        (alterative TIFF support) \*

        `pims\_nd2 <https://github.com/soft-matter/pims_nd2>`__ (improved Nikon

        .nd2 support)

        

        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
