`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.
`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](https://github.com/soft-matter/pims) framework, enabling easy access to multidimensional files, lazy slicing, and nice display in IPython.
The reader is written in the [pims](https://github.com/soft-matter/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](https://github.com/Open-Science-Tools/nd2reader).
### Documentation
### Documentation
The documentation is available [here](http://www.lighthacking.nl/nd2reader/).
Documentation specific to this fork is not available yet.
The documentation of the origianl `nd2reader` project was available [here](http://www.lighthacking.nl/nd2reader/).
### Installation
### Installation
The package is available on PyPi. Install it using:
The package is available on PyPi. Install it using:
```
```
pip install nd2reader
pip install zolfa-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.
If you don't already have the packages `numpy`, `pims` and `xmltodict`, they will be installed automatically running pip.
Python >= 3.5 are supported.
Python >= 3.10 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
### ND2s
`nd2reader` follows the [pims](https://github.com/soft-matter/pims) framework. To open a file and show the first frame:
`nd2reader` follows the [pims](https://github.com/soft-matter/pims) framework. To open a file and show the first frame:
@@ -58,13 +40,9 @@ with ND2Reader('my_directory/example.nd2') as images:
...
@@ -58,13 +40,9 @@ with ND2Reader('my_directory/example.nd2') as images:
After opening the file, all `pims` features are supported. Please refer to the [pims documentation](http://soft-matter.github.io/pims/).
After opening the file, all `pims` features are supported. Please refer to the [pims documentation](http://soft-matter.github.io/pims/).
#### Backwards compatibility
Older versions of `nd2reader` do not use the `pims` framework. To provide backwards compatibility, a legacy [Nd2](http://www.lighthacking.nl/nd2reader/nd2reader.html#module-nd2reader.legacy) class is provided.
### Contributing
### Contributing
If you'd like to help with the development of nd2reader or just have an idea for improvement, please see the [contributing](https://github.com/rbnvrw/nd2reader/blob/master/CONTRIBUTING.md) page
If you'd like to help with the development of nd2reader or just have an idea for improvement, please see the [contributing](https://gitlab.pasteur.fr/zolfa/zolfa-nd2reader/-/blob/master/CONTRIBUTING.md) page
for more information.
for more information.
### Bug Reports and Features
### Bug Reports and Features
...
@@ -74,6 +52,8 @@ If you get an unhandled exception, please paste the entire stack trace into the
...
@@ -74,6 +52,8 @@ If you get an unhandled exception, please paste the entire stack trace into the
### Acknowledgments
### Acknowledgments
First fork by Ruben Verweij.
PIMS modified version 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](http://finkelsteinlab.org/).
Original version by Jim Rybarski. Support for the development of this package was partially provided by the [Finkelstein Laboratory](http://finkelsteinlab.org/).
