Metadata-Version: 2.4
Name: SLAP2_UTILS
Version: 0.4.5
Summary: Code to support using a SLAP2 Microscope
Author-email: Peter Hogg <peterhogg2006@gmail.com>, Jerry Tong <jerrytong0810@gmail.com>
License: MPL-2.0
Project-URL: Homepage, https://github.com/Peter-Hogg/SLAP2_Utils
Project-URL: Issues, https://github.com/Peter-Hogg/SLAP2_Utils/issues
Classifier: License :: OSI Approved :: Mozilla Public License 2.0 (MPL 2.0)
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Operating System :: OS Independent
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: scipy
Requires-Dist: h5py
Requires-Dist: scikit-image
Requires-Dist: PyQT6
Requires-Dist: matplotlib
Requires-Dist: vispy
Requires-Dist: notebook
Requires-Dist: pyneurotrace
Requires-Dist: zarr
Requires-Dist: dask
Requires-Dist: napari
Requires-Dist: apoc
Provides-Extra: cupy
Requires-Dist: cupy; extra == "cupy"
Provides-Extra: cuda11x
Requires-Dist: cupy-cuda11x; extra == "cuda11x"
Provides-Extra: cuda12x
Requires-Dist: cupy-cuda12x; extra == "cuda12x"
Dynamic: license-file

# SLAP2_Utils
[![Tests](https://github.com/Peter-Hogg/SLAP2_Utils/actions/workflows/python-test.yml/badge.svg)](https://github.com/Peter-Hogg/SLAP2_Utils/actions/workflows/python-test.yml)[![Documentation](https://github.com/Peter-Hogg/SLAP2_Utils/actions/workflows/sphinx.yml/badge.svg)](https://peter-hogg.github.io/SLAP2_Utils/)
## Overview
The `SLAP2_Utils` library is designed to facilitate the reading of SLAP2 (Scanned Line Angular Projection Microscopy version 2) binary files using Python. This utility aims to support researchers and developers working with data from SLAP2 two-photon microscopes by providing an interface to manipulate and analyze these files directly in Python as an alternative to a Matlab-based workflow. The SLAP2 microscope is a commercially available kit from MBF Bioscience (https://www.mbfbioscience.com/products/slap2). The detailed documentation can be found by clicking the documentation icon above `Overview`.

## Features
- **Reading SLAP2 Binary Files**: Convert SLAP2 proprietary binary data into accessible formats for Python.
- **Metadata Parsing**: Extract and utilize metadata associated with SLAP2 data files.
- **Data Manipulation**: Tools to manipulate and process data points read from the binary file.
- **Trace Extraction**: Tools to extract and generate traces from ROIs imaged in integrated scan mode.
- **MatLab-based Visual Stimulus**: Different kinds of visual stimuli, from checkers and moving bars to visual stimuli utilized by the Allen Institute, are ready to be imported for a SLAP2-related experiment.
- **Motion Corrections**: GPU-based tools that allow calculation of motion drifts, with x, y, and z changes applied directly on the ROI inside the SLAP2 software (work in progress).


## Installation
Install with pip
```bash
pip install SLAP2-UTILS
```


Clone this repository

```bash
git clone https://github.com/Peter-Hogg/SLAP2_Utils.git
```
## Contributing

Contributions are welcome! If you'd like to contribute, please fork the repository and use a new branch for your contributions. Pull requests are welcome. Please report bugs, as we're still refining this library over time.

## License

This project is licensed under the Mozilla Public License Version 2.0 - see the LICENSE.md file for details.

## Credits and Acknowledgements
This library was developed by Peter Hogg and Jerry Tong. It's a rework of several Matlab tools from MBF with added utility functions. Thanks to all contributors who have helped in refining this tool and helped with the project.

