Metadata-Version: 2.1
Name: nbvv
Version: 1.0.0a0
Summary: Interactive volumetric voxel viewing
Home-page: https://github.com/allen-cell-animated/nbvv
Author: aics
Author-email: danielt@alleninstitute.org
License: UNKNOWN
Description: # Volume Viewer Jupyter Notebook Extension
        
        Embeds the Allen Institute web-based 3d viewer in Jupyter notebooks
        
        ---
        
        ## Description
        
        Most 3D viewers are far too heavyweight to use for quick visualization tasks when experimenting with tractably-sized (analyzing, checking, ...) 3D volumetric datasets. nbvv is a multichannel volume viewer for interactive data exploration in jupyter. This is a jupyter widget that provides volumetric rendering given a multiple channel zstack as a numpy array.
        
        Envisioned user group is anyone who wants a robust and quick way to interactively interrogate volumetric data as part of their workflows; domain which motivated development is multi-channel volumetric light/fluorescence microscopy datasets. The viewer is optimized for volume data that has finer xy resolution than z resolution.
        
        ## Installation
        
        To install from source:
        You will need to make sure nodejs and npm are installed on your system.
        One way to do this is using `nvm`, for example:
        `nvm install 14.17.0`
        `nvm use 14.17.0`
        Make sure you have jupyter notebook and nbextensions installed (not necessary in every environment):
        `pip install jupyter_contrib_nbextensions && jupyter contrib nbextension install --user`
        Then you can run `build.sh` from this repo, or:
        `pip install .`
        
        To install from pypi (not yet!) install the package:
        `pip install nbvv`
        and then enable the extension in jupyter:
        `jupyter nbextension install --py nbvv --sys-prefix`
        `jupyter nbextension enable nbvv --py --sys-prefix`
        
        ## Documentation
        
        If you have more extensive technical documentation (whether generated or not), ensure they are published to the following address:
        For full package documentation please visit
        [allen-cell-animated.github.io/nbvv](https://allen-cell-animated.github.io/nbvv/index.html).
        
        ## Quick Start
        
        try the demo notebook:
        `jupyter notebook examples/demo.ipynb`
        
        In a Jupyter notebook, load or create volume data in a numpy array.
        The data should be of shape (Z,Y,X) or (C,Z,Y,X) for multi-channel data.
        Display the numpy data using
        `import nbvv`
        `nbvv.volshow(mynumpydata, spacing=(1.0, 1.0, 4.0))`
        
        ## Development
        
        See [CONTRIBUTING.md](CONTRIBUTING.md) for information related to developing the code.
        
Keywords: ipython,jupyter,widgets
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Framework :: IPython
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Multimedia :: Graphics
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
