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canalysis-1.0.0
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مشاهده بیشترتوضیحات
This project provides a structure to integrate calcium traces and events, perform statistical analysis, make graphs and do classification problems to further understand the dataset.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | canalysis-1.0.0 |
| نام | canalysis |
| نسخه کتابخانه | 1.0.0 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Flynn OConnell |
| ایمیل نویسنده | Flynn OConnell <FlynnOConnell@gmail.com> |
| آدرس صفحه اصلی | - |
| آدرس اینترنتی | https://pypi.org/project/canalysis/ |
| مجوز | MIT License Copyright (c) 2022 Flynn OConnell Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
<h1> Calcium Imaging Data Analysis </h1>
<p>
<img style="float: right"
width="550"
height="300"
src=https://i.imgur.com/SPok8sB.gif
>
</p>
*Images from poster presented at AChems 2022 [[1]](#1).
###### **This project takes `.csv` files gathered from Inscopix Data Processing software for processing:**
* Syncing traces with externally captured GPIO events.</li>
* General <img src="https://latex.codecogs.com/svg.image?\Delta&space;F/F" /> based statistics.</li>
* Plotting: animated, 2D and 3D scatter, regression, skree, heatmap and correlation matrix.</li>
* Dimensionality reduction with variance filters and principal component analysis.</li>
* Support Vector Machine Learning for classification tasks.</li>
[](https://github.com/NeuroPyPy/CalciumAnalysis/blob/master/LICENSE)
[](https://www.codefactor.io/repository/github/neuropypy/calciumanalysis)
<table>
<tr >
<td nowrap><strong>Supported OS</strong></td>
<td>Linux (list of <a href="./docs/POSIX.md#the-list-of-posix-api-used-in-areg-sdk-including-multicast-message-router" alt="list of POSX API">POSIX API</a>), Windows 7 and higher.</td>
</tr>
</table>
---
### Directory Structure
For data loading, directories should be formatted a particular way that can be easily
modified by configuring `data.data_utils.file_handler`.
```bash
./data/
├── Animal 1
│ ├── Day 1
│ │ ├── *Events.csv
│ │ └── *Traces.csv
│ └── Day 2
│ ├── *Events.csv
│ └── *Traces.csv
├── Animal 2
│ └── Day 1
│ ├── *Events.csv
│ └── *Traces.csv
└── Animal 3
└── Day 1
├── *Events.csv
└── *Traces.csv
```
---
### Parameters and Directories
A configuration file `config.yaml` contains defaults that can be set in a single top-level file.
1. `DIRS:` - directories for loading and saving data
```yaml
DIRS:
data_dir: '/Users/me/mydata' # os is internally handled
save_stats: '~./home' # save statistical output
save_figs: '~/graphs' # can have multiple sub-dirs
save_nn: '~/svm' # train/test/eval scores from neural network
```
3. `SESSION:` - session instance information
```yaml
SESSION:
animal: 'animal_ID' # must include char + num
date: '123456' # must include all nun
dir: '/my/data' # must include / or \
```
3. `COLORS:` - event : color pairing
```yaml
COLORS:
Event1: 'color'
Event2: 'color'
Event3: 'color'
# from matplotlib.colors API
```
4. `DECODER:` - Decode GPIO signals into events
```yaml
DECODER:
Event1: 1, 2, 3, 4
Event2: 1, 3, 4
Event3: 1, 2, 3
Event4: 1, 4
# see data/data_utils/gpio_data.py for implementation
```
---
---
### **TO DO:**
* Additional layers to neural network for additional feature extraction
* Layer for additional outlier/anomaly detection
* Layer for linear trend normalization
* Any additional feature extraction layers i.e. temporal coding [[2]](#2), latency, duration, etc.
* Incorperate dataflow-based modeling design i.e. mapping actors to threads and the vectorization of actors (see [[3]](#3))
* Format all docstrings to NumPy style
#### References
<a id="1">[1]</a>
Long Term In-Vivo One-Photon Ca2+ Imaging of Taste-Responsive Cells In The Parabrachial Pons In The Freely Licking Rat.
Flynn P. O'Connell1, Joshua D. Sammons2, Patricia M. Di Lorenzo1. 1Binghamton University, Binghamton, NY, USA. 2University of Alabama at Birmingham, Birmingham, AL, USA. [Achems.org](https://achems.org/web/)
<a id="2">[2]</a>
Hallock R. M., Di Lorenzo P. M. (2006). Temporal coding in the gustatory system. Neurosci. Biobehav. Rev. 30, 1145–1160. [10.1016/j.neubiorev.2006.07.005](https://www.sciencedirect.com/science/article/abs/pii/S0149763406000741)
<a id="3">[3]</a>
Kyunghun Lee, Xiaomin Wu, Yaesop Lee, Da-Ting Lin, Shuvra S. Bhattacharyya & Rong Chen (2021) Neural decoding on imbalanced calcium imaging data with a network of support vector machines, Advanced Robotics, 35:7, 459-470, [DOI: 10.1080/01691864.2020.1863259](https://www.tandfonline.com/doi/abs/10.1080/01691864.2020.1863259?journalCode=tadr20)
نیازمندی
| مقدار | نام |
|---|---|
| >=2.8.1 | python-dateutil |
| >=2020.1 | pytz |
| >=1.18.5 | numpy |
| >=1.19.2 | numpy |
| >=1.20.0 | numpy |
| >=1.21.0 | numpy |
| >=6.0 | pytest |
| >=2.0 | pytest-cov |
| >=0.910 | mypy |
| >=3.9 | flake8 |
| >=3.24 | tox |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.0 | Python |
نحوه نصب
نصب پکیج whl canalysis-1.0.0:
pip install canalysis-1.0.0.whl
نصب پکیج tar.gz canalysis-1.0.0:
pip install canalysis-1.0.0.tar.gz