The AnnotAid AI Backend, built on FastAPI, offers a range of deep learning techniques to enhance the annotation process in the AnnotAid annotation tool. It facilitates the annotation of cells or more complex structures and offers assistance in evaluating individual criteria of the Nottingham Grading System.
+---.github # Github workflows
| +---workflows
+---.vscode # VSCode settings
+---docker # Backend and Celery worker dockerfiles
+---models # Downloaded weights
+---scripts
| +---api # Scripts for backend
| +---production # Scripts for production deployment
| +---weights # Scripts used to download model weights
+---slides # WSI images
+---src
| +---alembic
| | +---versions # Database migrations
| +---api # API endpoints
| | +---api_v1
| | | +---endpoints
| +---celery
| | +---active_learning # Active learning tasks
| | +---mc # Mitotic count tasks
| | +---np # Nuclear pleomoprhism tasks
| | +---nuclick # NuClick tasks
| | +---sam # SAM tasks
| | +---shared # Shared tasks
| +---core # Configuration files
| +---examples # Sample images used in documentation
| +---models
| | +---mc # Mitotic count models
| | +---np # Nuclear pleomorphism models
| | +---nuclick # NuClick model
| +---schemas # Validation schemas
| +---scripts
| +---utils
+---tests
| .env # Environment variables
| .env.example # Example template of environment variables
| .flake8 # Flake8 config
| .pre-commit-config.yaml # Pre-commit config
| alembic.ini # Alembic config
| Makefile # Project makefile
| mypy.ini # Mypy config
| pyproject.toml # Project config
Make sure you have the following tools installed before setting up the project:
Clone the repository:
git clone https://github.com/histopathology-image-annotation-tool/annotaid-ai-backend AnnotAidAIBE
cd AnnotAidAIBE
Create a Virtual Environment:
make venv
cp .env.example .env
If you want to use active learning, you need to download a sample VSI image or put custom images into pre-configured folder specified in the .env file.
make download_weights
make run env=dev
Instructions for production setup can be found in README.md.
AnnotAid AI Backend by Adam Bublavý is licensed under a GNU Affero General Public License v3.0 or later.