[ref] shape_embed

README.md

@@ -1,98 +0,0 @@
-# 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.
-
-[![Build Status](https://img.shields.io/badge/build-passing-green.svg)](https://github.com/ctr26/bioimage_embed)
-[![Python Version](https://img.shields.io/badge/python-3.7+-blue.svg)](https://github.com/ctr26/bioimage_embed)
-[![License](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/ctr26/bioimage_embed)
-
----
-
-## 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:
-
-```bash
-pip install bioimage_embed
-```
-
-### From GitHub:
-
-```bash
-pip install git+https://github.com/ctr26/bioimage_embed
-```
-
----
-
-## Usage
-
-### 1. Basic Installation:
-
-```bash
-pip install -e .
-```
-
-### 2. Command Line Interface (CLI):
-
-To get a list of all commands and functions:
-
-```bash
-bioimage_embed --help
-```
-
-OR
-
-```bash
-bie --help
-```
-
-### 3. Fetching Data:
-
-This utility makes it simple to fetch the necessary datasets:
-
-```bash
-make download.data
-```
-If you don't have a Kaggle account you must create one and then follow the next steps:
-1. Install the Kaggle API package so you can download the data from the Makefile you have all the information in their [Github repository](https://github.com/Kaggle/kaggle-api).
-2. To use the Kaggle API you need also to create an API token.
-   You can found how to do it in their [documentation](https://github.com/Kaggle/kaggle-api#api-credentials)
-4. After that you will need to add your user and key in a file called `kaggle.json` in this location in your home directory `chmod 600 ~/.kaggle/kaggle.json`
-5. Don't forget to accept the conditions for the "2018 Data Science Bowl" on the Kaggle website.
-   Otherwise you would not be able to pull this data from the command line. 
-
-### 4. 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:
-
-```bash
-poetry env use python
-poetry install
-poetry shell
-```
-
----
-
-## Support & Contribution
-
-For any issues, please refer to our [issues page](https://github.com/ctr26/bioimage_embed/issues). 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](https://github.com/ctr26/bioimage_embed/LICENSE) for more details.
-
----
-
-Happy Embedding! 🧬🔬