update-readme

Author: rkarmaka

.gitignore

@@ -8,5 +8,4 @@ envs
 # Ignore test files
 /biaqc/test.ipynb
 /biaqc/nd2_metadata_new.csv
-/biaqc/__pycache__/
-/tests/__pycache__/
+*.pyc

.vscode/settings.json

@@ -0,0 +1,11 @@
+{
+    "python.testing.unittestArgs": [
+        "-v",
+        "-s",
+        "./tests",
+        "-p",
+        "test_*.py"
+    ],
+    "python.testing.pytestEnabled": false,
+    "python.testing.unittestEnabled": true
+}

CONTRIBUTING.md

@@ -0,0 +1,55 @@
+# Contributing to Bio-image Analysis Quality Control
+
+Thank you for considering contributing to this project! We welcome contributions from the community and are grateful for your support.
+
+## How to Contribute
+
+### Reporting Bugs
+
+If you find a bug, please report it by opening an issue on our [GitHub Issues](https://github.com/rkarmaka/BIA-QC/issues) page. Include as much detail as possible to help us understand and reproduce the issue.
+
+### Suggesting Features
+
+We welcome suggestions for new features. Please open an issue on our [GitHub Issues](https://github.com/rkarmaka/BIA-QC/issues) page and describe the feature you would like to see, along with any relevant use cases.
+
+### Submitting Pull Requests
+
+1. **Fork the Repository**: Click the "Fork" button on the top right of the repository page to create a copy of the repository on your GitHub account.
+
+2. **Clone the Forked Repository**: Clone your forked repository to your local machine.
+    ```sh
+    git clone https://github.com/rkarmaka/BIA-QC.git
+    ```
+
+3. **Create a Branch**: Create a new branch for your feature or bug fix.
+    ```sh
+    git checkout -b feature-or-bugfix-name
+    ```
+
+4. **Make Changes**: Make your changes to the codebase.
+
+5. **Commit Changes**: Commit your changes with a descriptive commit message.
+    ```sh
+    git commit -m "Description of the changes"
+    ```
+
+6. **Push Changes**: Push your changes to your forked repository.
+    ```sh
+    git push origin feature-or-bugfix-name
+    ```
+
+7. **Open a Pull Request**: Go to the original repository and open a pull request. Provide a clear description of the changes and any relevant information.
+
+### Code Style
+
+Please follow the existing code style and conventions used in the project. This helps maintain consistency and readability.
+
+### Testing
+
+Ensure that your changes do not break existing tests and, if applicable, add new tests for your changes. Run the tests locally before submitting your pull request.
+
+### Documentation
+
+If your changes affect the documentation, please update the relevant documentation files accordingly.
+
+Thank you for your contributions!

README.md

@@ -1,2 +1,53 @@
 # Bio-image Analysis Quality Control
-This repo contains python package to perform automatic quality control for bioimage analysis.
+
+This repository contains a Python package to perform automatic quality control for bioimage analysis.
+
+## Table of Contents
+
+- [Installation](#installation)
+- [Usage](#usage)
+- [Features](#features)
+- [Examples](#examples)
+- [Contributing](#contributing)
+- [License](#license)
+
+## Installation
+
+To install the required dependencies, run:
+
+```sh
+pip install -r [requirements.txt](requirements.txt)
+```
+
+## Usage
+
+To use the package, you can run the main application:
+
+```sh
+python biaqc-app.py
+```
+
+### GUI
+
+The main graphical user interface (GUI) can be accessed by running the `biaqc-app.py` script. The GUI allows you to open folders, run analysis, and visualize results.
+
+
+## Features
+
+- **Automatic Quality Control**: Perform automatic quality control for bioimage analysis.
+- **Feature Extraction**: Extract features from bioimages.
+- **Metadata Analysis**: Analyze metadata associated with bioimages.
+- **Graphical User Interface**: User-friendly GUI for easy interaction.
+- **CSV Support**: Load and save results in CSV format.
+
+<!-- ## Examples
+
+Example usage of the package can be found in the [examples](examples/example_usage.py) directory. -->
+
+## Contributing
+
+Contributions are welcome! Please see the [CONTRIBUTING.md](CONtributing.md) file for guidelines on how to contribute to this project.
+
+## License
+
+This project is licensed under the MIT License. See the [LICENSE](LICENSE) file for more details.

_assets/icon.ico

@@ -239,7 +239,6 @@ def extract_all_features(self):
         }
 
 
-
 class Noise:
     image: np.ndarray | None = None