zolfa-nd2reader 3.4.0

A tool for reading ND2 files produced by NIS Elements

zolfa-nd2reader

About

zolfa-nd2reader is a pure-Python package that reads images produced by NIS Elements 4.0+. It has only been definitively tested on NIS Elements 4.30.02 Build 1053. Support for older versions is being actively worked on. The reader is written in the pims framework, enabling easy access to multidimensional files, lazy slicing, and nice display in IPython.

This version is a fork of the project of published here.

Documentation

Documentation specific to this fork is not available yet.

The documentation of the origianl nd2reader project was available here.

Installation

The package is available on PyPi. Install it using:

pip install zolfa-nd2reader

If you don't already have the packages numpy, pims and xmltodict, they will be installed automatically running pip. Python >= 3.10 are supported.

ND2s

nd2reader follows the pims framework. To open a file and show the first frame:

from zolfa.nd2reader import ND2Reader
import matplotlib.pyplot as plt

with ND2Reader('my_directory/example.nd2') as images:
  plt.imshow(images[0])

After opening the file, all pims features are supported. Please refer to the pims documentation.

Contributing

If you'd like to help with the development of nd2reader or just have an idea for improvement, please see the contributing page for more information.

Bug Reports and Features

If this fails to work exactly as expected, please open an issue. If you get an unhandled exception, please paste the entire stack trace into the issue as well.

Acknowledgments

First fork by Ruben Verweij.

PIMS modified version by Ruben Verweij.

Original version by Jim Rybarski. Support for the development of this package was partially provided by the Finkelstein Laboratory.