pims-nd2 0.3

Dependencies

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.

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).