nd2reader

Simple access to .nd2 files

About

nd2reader is a pure-Python package that reads images produced by NIS Elements.

.nd2 files contain images and metadata, which can be split along multiple dimensions: time, fields of view (xy-plane), focus (z-plane), and filter channel.

nd2reader produces data in numpy arrays, which makes it trivial to use with the image analysis packages scikit-image and OpenCV.

Installation

Just use pip:

pip install nd2reader

If you want to install via git, clone the repo and run:

python setup.py install

Usage

nd2reader provides two main ways to view image data. For most cases, you'll just want to iterate over each image:

import nd2reader
nd2 = nd2reader.Nd2("/path/to/my_images.nd2")
for image in nd2:
    do_something(image.data)

If you have complicated hierarchical data, it may be easier to use image sets, which groups images together if they share the same time index and field of view:

import nd2reader
nd2 = nd2reader.Nd2("/path/to/my_complicated_images.nd2")
for image_set in nd2.image_sets:
    # you can select images by channel
    gfp_image = image_set.get("GFP")
    do_something_gfp_related(gfp_image)

    # you can also specify the z-level. this defaults to 0 if not given
    out_of_focus_image = image_set.get("Bright Field", z_level=1)
    do_something_out_of_focus_related(out_of_focus_image)

Image objects provide several pieces of useful data.

>>> import nd2reader
>>> nd2 = nd2reader.Nd2("/path/to/my_images.nd2")
>>> image = nd2.get_image(14, 2, "GFP", 1)
>>> image.data
array([[1809, 1783, 1830, ..., 1923, 1920, 1914],
       [1687, 1855, 1792, ..., 1986, 1903, 1889],
       [1758, 1901, 1849, ..., 1911, 2010, 1954],
       ...,
       [3363, 3370, 3570, ..., 3565, 3601, 3459],
       [3480, 3428, 3328, ..., 3542, 3461, 3575],
       [3497, 3666, 3635, ..., 3817, 3867, 3779]])
>>> image.channel
'GFP'
>>> image.timestamp
1699.7947813408175
>>> image.field_of_view
2
>>> image.z_level
1

You can also get a quick summary of image data.

>>> image
<ND2 Image>
1280x800 (HxW)
Timestamp: 1699.79478134
Field of View: 2
Channel: GFP
Z-Level: 1