Jim Rybarski 524ec8de84 | 10 years ago | |
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nd2reader | 10 years ago | |
tests | 10 years ago | |
.gitignore | 10 years ago | |
CONTRIBUTORS.txt | 10 years ago | |
Dockerfile | 10 years ago | |
LICENSE.txt | 10 years ago | |
Makefile | 10 years ago | |
README.md | 10 years ago | |
requirements.txt | 10 years ago | |
setup.cfg | 10 years ago | |
setup.py | 10 years ago | |
tests.py | 10 years ago |
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 such as scikit-image
and OpenCV
.
Just use pip (numpy
is required):
pip install numpy nd2reader
If you want to install via git, clone the repo and run:
pip install numpy
python setup.py install
A quick summary of ND2 metadata can be obtained as shown below.
>>> import nd2reader
>>> nd2 = nd2reader.Nd2("/path/to/my_images.nd2")
>>> nd2
<ND2 /path/to/my_images.nd2>
Created: 2014-11-11 15:59:19
Image size: 1280x800 (HxW)
Image cycles: 636
Channels: '', 'GFP'
Fields of View: 8
Z-Levels: 3
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)
There is a method, get_image
, which allows random access to images. This might not always return an image, however,
if you acquired different numbers of images in each cycle of a program. For example, if you acquire GFP images every
other minute, but acquire bright field images every minute, get_image
will return None
at certain time indexes.
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
If this fails to work exactly as expected, please open a Github issue. If you get an unhandled exception, please paste the entire stack trace into the issue as well.
Please feel free to submit a pull request with any new features you think would be useful. You can also create an issue if you'd just like to propose or discuss a potential idea.
Support for the development of this package was provided by the Finkelstein Laboratory.