# neuronVis

**Repository Path**: hghgiteecode/neuron-vis

## Basic Information

- **Project Name**: neuronVis
- **Description**: analyse tool for mouse neuron
- **Primary Language**: Unknown
- **License**: Not specified
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 6
- **Created**: 2025-03-27
- **Last Updated**: 2025-03-27

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

论文链接：https://www.nature.com/articles/s41593-025-01919-0
###所有 3D 神经元展示均使用自行开发的 Python 包“neuron-vis”  （https://gitee.com/bigduduwxf/neuron-vis） 绘制。
###颜色随机分配给以群体水平绘制的单个神经元。
 

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


## NeuronVis is a tool for mouse neuron analyse 

| = | = |
| ---- | ---- |
| 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 analyse .

# USAGE


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

* Download the resource from http://bap.cebsit.ac.cn/bap/neuronVis/resource.zip and decompressed to the directory neuronvis  

* conda env create -f env.yml

* conda activate neuronVis

### Add the path of neuronVis to sys.path
    import sys
    sys.path.append(your git repository+"/neuronVis")

## Get Data Example
* https://gitee.com/bigduduwxf/neuron-vis/blob/master/analyseCase/getDataExample.ipynb

## Get all Data in ION (only allowed in ION, some samples are not public)
    in IONData.py line 19
    //self.ip='bap.cebsit.ac.cn'
    or :
    iondata.ip='10.10.48.110'

### Get neuron list by sampleid
    from IONData import  IONData 
    import SwcLoader
    iondata =IONData()
    neuronlist=iondata.getNeuronListBySampleID('192106')

### Get region list included in a region referenced to Allen
    br = BrainRegion()
	br.praseJson()
	subbr= br.getRegion('ORB')
	subbr.annotation()
	brproperty=RegionProperty(copy.deepcopy(subbr))
	brproperty.print()
	subbr.print()
	subbrlist=br.getRegionList('grv of CBX')

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

    from IONData import  IONData 
    import SwcLoader
    iondata =IONData()
    neuronlist=iondata.getNeuronListBySampleID('192106')
    swc = iondata.getNeuronByID('192106', '001.swc')
    pro = iondata.getNeuronPropertyByID('192106', '001.swc')
    print(pro)
    
### Get property of regions with subregions like 'HY'
    import BrainRegion as BR 
    br = BR.BrainRegion()
    br.praseJson()
    br.setProperty(pro['projectregion'])
    HYProjectLength = br.getSumProperty('HY')

### Parse neuron data into a tree

    from IONData import  IONData 
    import SwcLoader
    iondata =IONData()
    neuron = SwcLoader.NeuronTree()
    neuron.readSWC(iondata.getNeuronByID('192106', '001.swc'))
    
### Render region and swc and savepng

    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)

### Run the neuronVis/Flatmap.py to get flatmap

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

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

### Draw neuron somas on the flatmap
![test2 截图](https://gitee.com/bigduduwxf/neuron-vis/raw/master/resource/Somas_on_FlattenMap.png#pic_center)
```
#position is the array of soma positions in 3D space
iondata = IONData.IONData() #wxf
res,gridpath = iondata.getFileFromServer("boundlaplace20.nrrd")
grid,header = nrrd.read(gridpath)
resRelaxation,RelaxationPath=iondata.getFileFromServer('boundlaplaceout20.nrrd')
relaxation,relaxationheader = nrrd.read(RelaxationPath)
resdv0, dv0Path = iondata.getFileFromServer('dv0.nrrd')
dv0, dv0header = nrrd.read(dv0Path)
resdv1, dv1Path = iondata.getFileFromServer('dv1.nrrd')
dv1, dv1header = nrrd.read(dv1Path)
resdv2, dv2Path = iondata.getFileFromServer('dv2.nrrd')
dv2, dv2header = nrrd.read(dv2Path)
dv0 = dv0.astype(np.float32) / 1000 - 1
dv1 = dv1.astype(np.float32) / 1000 - 1
dv2 = dv2.astype(np.float32) / 1000 - 1
position=BL.ComputeStreamlines(grid,dv0,dv1,dv2,position)
flatenPara = Flatmap.createSurfaceGraph()
flattened_position=[]
for p in position:
    flattened_position.append(Flatmap.map2Flatmap(flatenPara,np.array(p[1])*2,True))
flatmapedge=cv.imread('flatmapedge2.tif',1)
flatmap=cv.imread('flatmap.tif',2)
color = np.array([np.random.rand() for i in range(300)]).reshape(100,3)*255
for p in flattened_position:
    cv.circle(flatmapedge, (int(p[0])*2, int(p[1])*2),15, color[flatmap[int(p[1])][int(p[0])]], -1)
plt.imshow(flatmapedge)
plt.show()
```

### Laplace's equation
All the glories of Laplace's equation for measuring cortical thickness
 as initially described in:

Jones SE, Buchbinder BR, Aharon I. Three-dimensional mapping of
cortical thickness using Laplace's equation. Hum Brain Mapp. 2000
Sep;11(1):12-32.

and modified somewhat in:

Lerch JP, Carroll JB, Dorr A, Spring S, Evans AC, Hayden MR, Sled JG,
Henkelman RM. Cortical thickness measured from MRI in the YAC128 mouse
model of Huntington's disease. Neuroimage. 2008 Jun;41(2):243-51.

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

### Cluster with some neuron figure/paper1figure5.py
Apply clustermap API of package seaborn to cluster data hierarchically.

```
    seaborn.clustermap(data, *, pivot_kws=None, method='average', metric='euclidean', z_score=None, standard_scale=None, figsize=(10, 10), cbar_kws=None, row_cluster=True, col_cluster=True, row_linkage=None, col_linkage=None, row_colors=None, col_colors=None, mask=None, dendrogram_ratio=0.2, colors_ratio=0.03, cbar_pos=(0.02, 0.8, 0.05, 0.18), tree_kws=None, **kwargs)
    Parameters
        data: Rectangular data for clustering.
        method: Linkage method to use for calculating clusters.
        metric: Distance metric to use for the data.
        {row,col}_cluster: If True, cluster the {rows, columns}.
```

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

### Save to svg
    import sys,copy,os
    sys.path.append(os.getcwd()+"/neuronVis")
    import json
    import matplotlib.pyplot as plt
    import numpy as np
    import IONData 
    import SwcLoader
    iondata =IONData.IONData()
    swc = iondata.getNeuronByID('192106', '033.swc')

    neuron = SwcLoader.NeuronTree()
    neuron.readSWC(swc)
    plt.figure(figsize=(12, 12))
    axes0 = plt.subplot(111)
    plt.axis('off')
    axes0.set_xlim(0, 10000)
    axes0.set_ylim(0, 10000)
    # plt.Circle((neuron.root.z, neuron.root.y), 300)
    for edge in neuron.edges:
        x=[]
        y=[]
        for p in edge:
            x.append(10000-p.z)
            y.append(10000-p.y)
        plt.plot(x, y,color='#FFDD44')
    # plt.figure(facecolor='gainsboro')
    plt.plot(10000-neuron.root.z,10000- neuron.root.y,'ob')


    plt.savefig(fname="./resource/neuron.svg",format="svg")
    plt.show()

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

Authors
=======

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

*Shou Qiu <sqiu@ion.ac.cn> 

*Le Gao <lgao@ion.ac.cn> 

*ZhuoLei Jiao <zljiao@ion.ac.cn> 



在使用 NeuronVis 查看自己的神经元数据时，可以通过以下步骤进行操作：

### 1. 准备数据
- **数据格式**：NeuronVis 支持多种数据格式，包括 SWC 格式的神经元数据。确保你的数据是 SWC 格式，或者可以将其转换为 SWC 格式。
- **数据存储路径**：将你的神经元数据存储在 NeuronVis 项目目录下的 `resource` 文件夹中。

### 2. 环境配置
- 克隆 NeuronVis 项目：
  ```bash
  git clone https://gitee.com/bigduduwxf/neuron-vis.git
  ```
- 创建并激活 Python 环境：
  ```bash
  conda env create -f env.yml
  conda activate neuronVis
  ```
- 将 NeuronVis 的路径添加到 Python 的 `sys.path` 中：
  ```python
  import sys
  sys.path.append('/path/to/your/neuronVis')
  ```

### 3. 加载和处理数据
- 使用 `IONData` 类加载数据：
  ```python
  from IONData import IONData
  iondata = IONData()
  # 如果你的数据存储在本地，可以直接加载 SWC 文件
  neuron_data = iondata.getNeuronByID('sample_id', 'neuron_file.swc')
  ```
- 如果你的数据不在 ION 服务器上，可以直接从本地路径加载 SWC 文件。

### 4. 可视化数据
- 使用 `neuronVis` 类进行可视化：
  ```python
  import neuronVis as nv
  neuronvis = nv.neuronVis()
  neuronvis.addNeuron(neuron_data)
  neuronvis.render.savepng('output.png')
  neuronvis.render.run()
  ```
- 如果需要查看神经元的特定属性，可以使用 `BrainRegion` 类来解析和处理。

### 5. 高级功能
- **生成扁平图（Flatmap）**：可以使用 NeuronVis 提供的 Flatmap 功能将神经元投影到扁平图上。
- **聚类分析**：使用 `seaborn` 或其他数据分析工具对神经元数据进行聚类分析。

通过以上步骤，你可以将自己的神经元数据加载到 NeuronVis 中进行处理和可视化。如果需要更详细的指导，可以参考 NeuronVis 的官方文档。