Metadata-Version: 1.1
Name: pims-nd2
Version: 0.3
Summary: ND2SDK wrapper for PIMS
Home-page: https://github.com/soft-matter/pims_nd2
Author: Casper van der Wel
Author-email: caspervdw@gmail.com
License: UNKNOWN
Download-URL: https://github.com/soft-matter/pims_nd2/tarball/0.3
Description: pims\_nd2

        =========

        

        This package lets `pims <https://github.com/soft-matter/pims>`__

        interface with the `ND2SDK <http://www.nd2sdk.com>`__ for fast reading

        of Nikon \*.nd2 files.

        

        This is implemented on Windows and Linux systems. An SDK for OSX is

        already included, this is probably easy to implement.

        

        Dependencies

        ------------

        

        This reader is based on ``pims.FramesSequenceND``, which is available

        from version 0.3. Apart from

        `pims <https://github.com/soft-matter/pims>`__ there are no extra

        dependencies. The required c libraries are included and will be added to

        the PATH variable at runtime.

        

        Examples

        --------

        

        The following code opens the demo file included in the package and

        iterates through the first 3 frames. Note that frames are only read when

        necessary.

        

        ::

        

            from pims_nd2 import ND2_Reader

            with ND2_Reader('cluster.nd2') as frames:

                frames.iter_axes = 't'

                frames.bundle_axes = 'zyx'

                frames.default_coords['c'] = 1

                for frame in frames[:3]:

                    # do something with 3D frames in channel 1

        

        The best way to use the reader is using a context manager. If you do not

        use a context manager, make sure to call ``frames.close()`` at the end

        of your script.

        

        Metadata access can be done on two levels: reader level and frame level.

        

        ::

        

            frames.metadata['mpp']  # calibration in microns per pixel

            frames[0].metadata['t_ms']  # timestamp of image in milliseconds

        

        Supporting Grant

        ----------------

        

        This reader was developed by Casper van der Wel, as part of his PhD

        thesis work in Daniela Kraftâ€™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).

        
Platform: Operating System :: Microsoft :: Windows :: Windows 7
Platform: Operating System :: Microsoft :: Windows :: Windows Vista
Platform: Operating System :: POSIX :: Linux
