Metadata-Version: 2.0
Name: PIMS
Version: 0.4.1
Summary: Python Image Sequence
Home-page: https://github.com/soft-matter/pims
Author: PIMS Contributors
Author-email: dallan@pha.jhu.edu
License: UNKNOWN
Platform: UNKNOWN
Requires-Dist: numpy (>=1.7)
Requires-Dist: six (>=1.8)
Requires-Dist: slicerator (>=0.9.7)

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) \* `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)

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


