nd2reader
Pure Python library for reading NIS Elements ND2 images and metadata
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
2 of 12 committers (16.7%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.2%) to scientific vocabulary
Keywords
Repository
Pure Python library for reading NIS Elements ND2 images and metadata
Basic Info
- Host: GitHub
- Owner: Open-Science-Tools
- License: gpl-3.0
- Language: Python
- Default Branch: master
- Homepage: https://open-science-tools.github.io/nd2reader/
- Size: 27.1 MB
Statistics
- Stars: 47
- Watchers: 4
- Forks: 31
- Open Issues: 29
- Releases: 17
Topics
Metadata Files
README.md
nd2reader
This package is no longer actively developed because I'm no longer working in this field and can't properly maintain it. If you'd like to help, please see the contributing page for more information.
About
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.
Alternatives
- nd2
- Open a PR if you'd like to be listed here.
Documentation
The documentation is available here.
Installation
The package is available on PyPi. Install it using:
pip install nd2reader
If you don't already have the packages numpy, pims, six and xmltodict, they will be installed automatically if you use the setup.py script.
Python >= 3.5 are supported.
Installation via Conda Forge
Installing nd2reader from the conda-forge channel can be achieved by adding conda-forge to your channels with:
conda config --add channels conda-forge
Once the conda-forge channel has been enabled, nd2reader can be installed with:
conda install nd2reader
It is possible to list all of the versions of nd2reader available on your platform with:
conda search nd2reader --channel conda-forge
ND2s
nd2reader follows the pims framework. To open a file and show the first frame:
```python from 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.
Backwards compatibility
Older versions of nd2reader do not use the pims framework. To provide backwards compatibility, a legacy Nd2 class is provided.
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
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.
Owner
- Name: Open Science Tools
- Login: Open-Science-Tools
- Kind: organization
- Repositories: 2
- Profile: https://github.com/Open-Science-Tools
GitHub Events
Total
- Create event: 1
- Release event: 1
- Issues event: 3
- Watch event: 2
- Issue comment event: 5
- Push event: 8
- Pull request event: 3
- Fork event: 1
Last Year
- Create event: 1
- Release event: 1
- Issues event: 3
- Watch event: 2
- Issue comment event: 5
- Push event: 8
- Pull request event: 3
- Fork event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Jim Rybarski | j****m@r****m | 220 |
| Ruben Verweij | v****j@p****l | 126 |
| Gabriele Girelli | g****0@g****m | 27 |
| Ruben Verweij | r****w | 26 |
| Ruben Verweij | r****n@l****l | 24 |
| unknown | w****1@c****u | 4 |
| Gregor Lichtner | g****r@c****e | 4 |
| Ruben Verweij | d****t@r****l | 3 |
| Jim Rybarski | j****m@d****m | 1 |
| Ulugbek Abdullaev | u****a@g****m | 1 |
| William Niu | 8****u | 1 |
| jbf81tb | j****b@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 2
- Total pull requests: 3
- Average time to close issues: over 1 year
- Average time to close pull requests: over 1 year
- Total issue authors: 2
- Total pull request authors: 3
- Average comments per issue: 1.5
- Average comments per pull request: 1.33
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- zhouchunyuan (1)
- henriquenunez (1)
Pull Request Authors
- aarpon (1)
- mansouralawi (1)
- vinsfan368 (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- numpy >=1.14
- pims >=0.3.0
- six >=1.4
- xmltodict >=0.9.2
- numpy >=1.14
- pims >=0.3.0
- six >=1.4
- xmltodict >=0.9.2