Metadata-Version: 2.1
Name: megafish
Version: 0.1.1
Summary: Multi-omics Extensible GPU-Accelerated FISH analysis framework
Author-email: Yuma Ito <yumaitou@outlook.com>
License: BSD 3-Clause License
        
        Copyright (c) 2024, Yuma Ito
        
        Redistribution and use in source and binary forms, with or without
        modification, are permitted provided that the following conditions are met:
        
        1. Redistributions of source code must retain the above copyright notice, this
           list of conditions and the following disclaimer.
        
        2. Redistributions in binary form must reproduce the above copyright notice,
           this list of conditions and the following disclaimer in the documentation
           and/or other materials provided with the distribution.
        
        3. Neither the name of the copyright holder nor the names of its
           contributors may be used to endorse or promote products derived from
           this software without specific prior written permission.
        
        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
        
Classifier: Programming Language :: Python :: 3.11
Requires-Python: <3.12,>=3.11
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: matplotlib
Requires-Dist: dask
Requires-Dist: xarray
Requires-Dist: zarr
Requires-Dist: scikit-image
Requires-Dist: scikit-learn
Requires-Dist: tifffile
Requires-Dist: scipy
Requires-Dist: napari[all]
Requires-Dist: imaris-ims-file-reader
Provides-Extra: cpu
Requires-Dist: numpy; extra == "cpu"

# MEGA-FISH

MEGA-FISH (Multi-omics Extensible GPU-Accelerated FISH analysis framework) is a Python package designed to process large-scale fluorescence images for spatial omics applications, including SeqFISH, SeqIS, and decoding-based FISH methods.

MEGA-FISH stitches sequentially captured tile images into a large, chunked single image and utilizes efficient computational resources (GPU or multi-threaded/multi-process CPU) for each processing step.

Users can generate a cell-by-gene expression matrix by combining simple functions such as image registration, segmentation, and spot detection.

Please see documentation for more information about MEGA-FISH.

## Installation

MEGA-FISH supports GPU acceleration on Linux systems and Windows PCs with WSL2.
See the [documentation](https://megafish.readthedocs.io/en/latest/installation.html) for more information.

MEGA-FISH supports multi-core CPU parallel computation and is available on Linux, Windows, and macOS. Below are the installation steps for setting up CPU-only MEGA-FISH.

```bash
conda create -n megafish python=3.11
conda activate megafish
pip install megafish
```

## Getting Started

Once you have installed MEGA-FISH, you can start by following the [tutorial](https://megafish.readthedocs.io/en/latest/tutorial.html) using the example data. 

## Data Structure

MEGA-FISH is designed not to create a MEGA-FISH-specific data structure, but to use simple naming rules for xarray. This allows users to easily customize the analysis pipeline and transfer the data to other packages. See the [documentation](https://megafish.readthedocs.io/en/latest/) for the data structure and functions.

## Contributing

We welcome contributions to MEGA-FISH. Please see the [contribution guide](https://megafish.readthedocs.io/en/latest/contributing.html) for more information.

## Citing

If MEGA-FISH was useful for your research, please consider citing the following our paper:

Coming soon.

## License

MEGA-FISH is licensed under the [BSD 3-Clause License](https://github.com/yumaitou/slitflow/blob/main/LICENCE). 


