Metadata-Version: 2.1
Name: fly2p
Version: 0.2.1
Summary: Tools for analyzing 2p (calcium) imaging data collected in flies (or other insects).
License: MIT
Author: hjmh
Author-email: hjmhaberkern@gmail.com
Requires-Python: >=3.8,<4.0
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Requires-Dist: Shapely (>=1.7.1,<2.0.0)
Requires-Dist: anywidget (==0.4.2)
Requires-Dist: h5py (>=3.1.0,<4.0.0)
Requires-Dist: imjoy (>=0.11.20,<0.12.0)
Requires-Dist: ipywidgets (==8.1.1)
Requires-Dist: matplotlib (>=3.3.3,<4.0.0)
Requires-Dist: napari (>=0.4.3,<0.5.0)
Requires-Dist: pandas (>=1.2.1,<2.0.0)
Requires-Dist: pyyaml (>=6.0.1)
Requires-Dist: scanimage-tiff-reader (>=1.4.1)
Requires-Dist: scikit-image (>=0.19.3,<0.20.0)
Requires-Dist: scikit-learn (>=1.1.3,<2.0.0)
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Description-Content-Type: text/markdown

<img src="https://user-images.githubusercontent.com/10639803/126242184-65bc84c4-3fa2-4034-be51-3e8c2e4d9f8c.png" align="middle" width="3000"/>

# fly2p

Tools for analyzing imaging data collected with [Vidrio Scanimage software](https://vidriotechnologies.com/scanimage/) or [micromanger](https://micro-manager.org/). Loading ScanImage data relies on [scanimageReader](https://pypi.org/project/scanimage-tiff-reader/), which can be installed via 'pip install scanimage-tiff-reader'. Other dependencies are tracked using poetry.

### Organization
The fly2p package contains the following submodules:
* **preproc**: Some file-format specific functions that extract metadata and load the imaging data. imgPreproc.py defines a data object to hold metadata and imaging data as well as basic proporcessing functions.
* **viz**: A collection of utility functions related to plotting flourescence traces and images.

In addition, the **scripts** folder contains notebooks that illustrate how to use functions in this module based on example files in **sample** (sample files are not currently pushed to repo).

### Installation
I recommend using poetry to setup a custom conda environment. A helpful introduction can be found [here](https://ealizadeh.com/blog/guide-to-python-env-pkg-dependency-using-conda-poetry).

0. Clone repo, navigate into folder
1. If you don't already have poetry, [install poetry](https://python-poetry.org/docs/#installation). You may need to close command window and open a new one.
2. Create conda environment:  
 `conda create --name fly2p python=3.8`
4. Activate environment:  
 `conda activate fly2p`
6. Make sure you are in the top folder of the cloned repo, then install dependencies:  
 `poetry install`
8. Setup the new environment as an ipython kernel:  
    `conda install -c anaconda ipykernel`  
    then  
    `python -m ipykernel install --user --name=fly2p`

Now you should be able to run the example notebooks in the **scripts** folder without problems.

