This package lets pims interface with the ND2SDK 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.
This reader is based on pims.FramesSequenceND, which is available from version 0.3. Apart from pims there are no extra dependencies. The required c libraries are included and will be added to the PATH variable at runtime.
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
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).