pims-nd2 0.1

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.
Currently, this is only implemented for Windows.

SDKs for Linux and OSX are already included, these are probably easy to implement.

Dependencies
------------

This reader is based on `pims.FramesSequenceND`, which is available from version 0.3.0. 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 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).