# neuronVis

**Repository Path**: chen-shishuo/neuron-vis

## Basic Information

- **Project Name**: neuronVis
- **Description**: visualization library for mouse neuron based on vispy
- **Primary Language**: Unknown
- **License**: Not specified
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 5
- **Created**: 2022-05-13
- **Last Updated**: 2022-05-24

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README


# neuronVis



## visualization and analyse library for mouse neuron based on vispy 

| = | = |
| ---- | ---- |
| Contact | xfwang@ion.ac.cn|
| Date | 27 April 2022 |
| Copyright |  `GFDLv1.2+ <http://www.gnu.org/licenses/fdl.html>` |
 Version | 1.0 |

neuronVis is a tool for mouse neuron visualization which is based on vispy(gloo).

# USAGE


* git clone https://gitee.com/bigduduwxf/neuron-vis.git

* Download the resource from http://10.10.48.110/bap/other/resource.zip and decompressed to the directory neuronvis  


* conda env create -f env.yml

### Get swc and property form iondata by sampleid and neuron name

    from neuronVis.IONData import  IONData 
    from neuronVis import SwcLoader
    iondata =IONData()
    neuronlist=iondata.getNeuronListBySampleID('192106')
    swc = iondata.getNeuronByID('192106', '001.swc')
    pro = iondata.getNeuronPropertyByID('192106', '001.swc')
    neuron = SwcLoader.NeuronTree()
    neuron.readSWC(swc)
    print(pro)
    
### Render region and swc

    import sys
    # add the path 
    sys.path.append(r"the path of neuronVis")
    import neuronVis as nv

    neuronvis = nv.neuronVis()
    # neuronvis.render.setBackgroundColor((0.0,0.20,0.5,1.0))
    neuronvis.addRegion('CA2',[0.5,1.0,0.5])
    neuronvis.addNeuron('./resource/033.swc')
    neuronvis.render.savepng('resource/test.png')
    neuronvis.render.setView('posterior')
    # neuronvis.render.setLookAt()
    neuronvis.addNeuron('./resource/192092-012.swc',[1.0,1.0,0.0])
    neuronvis.addNeuronByID('192106','011.swc',[1.0,1.0,0.0])
    neuronvis.render.savepng('resource/test2.png')

    neuronvis.render
    nv.app.run()

![test2 截图](https://gitee.com/bigduduwxf/neuron-vis/raw/master/resource/test2.png#pic_center)



Authors
=======

*XiaoFei Wang <xfwang@ion.ac.cn>