| Name | nbvv JSON |
| Version |
1.6.2
JSON |
| download |
| home_page | |
| Summary | Interactive volumetric voxel viewing |
| upload_time | 2023-06-02 23:26:11 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | |
| license | Allen Institute Software License – This software license is the 2-clause BSD license plus clause a third clause that prohibits redistribution and use for commercial purposes without further permission. Copyright © 2020. Allen Institute. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Redistributions and use for commercial purposes are not permitted without the Allen Institute’s written permission. For purposes of this license, commercial purposes are the incorporation of the Allen Institute's software into anything for which you will charge fees or other compensation or use of the software to perform a commercial service for a third party. Contact terms@alleninstitute.org for commercial licensing opportunities. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
| keywords |
ipython
jupyter
volume rendering
widgets
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# 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 jupyterlab, jupyter notebook and nbextensions installed (not necessary in every environment):
```
pip install jupyter_contrib_nbextensions && jupyter contrib nbextension install --user
```
Install nbvv in one of these ways:
- Option 1: Install from PyPi
```
pip install nbvv
jupyter nbextension install --py nbvv --sys-prefix
jupyter nbextension enable nbvv --py --sys-prefix
```
- Option 2: Run `build.sh` from this repo
- Option 3: Step-by-step, from source:
```
pip install -e .
jupyter nbextension install --py --overwrite --symlink --sys-prefix nbvv
jupyter nbextension enable --py --sys-prefix nbvv
jupyter labextension develop . --overwrite
```
## Documentation
Extended documentation is not available yet. When completed it will be made available at: [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
```
or likewise with jupyterlab:
```
jupyter lab 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), channel_names=my_list_of_channel_name_strings)
```
`volshow` also provides an optional `viewer_height` parameter if you want to make the viewer larger in the notebook. Default is 500 and values should be specified in CSS pixels.
## Development
See [CONTRIBUTING.md](CONTRIBUTING.md) for information related to developing the code.
Raw data
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