bioimage_embed: Autoencoders for Biological Image Data

bioimage_embed is an all-in-one Python package designed to cater to the needs of computational biologists, data scientists, and researchers working on biological image data. With specialized functions to handle, preprocess, and visualize microscopy datasets, this tool is tailored to streamline the embedding process for biological imagery.

Features

• Seamless loading of microscopy datasets, compatible with the BioImage Data Resource and Cell Image Library.
• Built-in preprocessing functions to ensure your images are primed for encoding.
• Visual tools to dive deep into the encoding and decoding processes of your autoencoders.

Installation

To get started with bioimage_embed, you can install it directly via pip or from the GitHub repository.

From PyPI:

pip install bioimage_embed

From GitHub:

pip install git+https://github.com/ctr26/bioimage_embed

Usage

1. Basic Installation:

pip install -e .

2. Command Line Interface (CLI):

To get a list of all commands and functions:

bioimage_embed --help

OR

bie --help

3. Developer Installation:

For those intending to contribute or looking for a deeper dive into the codebase, we use poetry to manage our dependencies and virtual environments:

poetry env use python
poetry install
poetry shell

Support & Contribution

For any issues, please refer to our issues page. Contributions are more than welcome! Please submit pull requests to the master branch.

License

bioimage_embed is licensed under the MIT License. Please refer to the LICENSE for more details.

Happy Embedding! 🧬🔬