SlideTap Project

Overview

SlideTap is a comprehensive platform designed for managing and processing digital pathology images and metadata into research datasets. It provides tools for image preprocessing, metadata management, and project-based workflows. The platform is built using Flask for the web application, Celery for task scheduling and processing, and Node for the web client.

Features

  • Metadata Management: Allows importing, exporting, and curating of metadata.
  • Image Processing: Supports various image processing steps including DICOM conversion and metadata extraction.
  • Project Management: Facilitates the creation and management of projects, batches, and datasets.

Components

Web Client

The web client provides a graphical interface enabling the user to:

  • Login to the application
  • Create projects and batches
  • Search and curate metadata
  • Process images
  • Finalize projects into datasets

Web Application

The web application handles the requests from the web client:

  • User authentication and authorization
  • Project and batch management
  • Image and metadata processing

Task Processing

Long running tasks can be handled in the background using tasks:

  • Metadata import and export
  • Image preprocessing and postprocessing

Dataset and Site-Specific Implementation

The platform can, and must, be adopted to the type of dataset to create and the site to extract metadata and images from:

  • A schema is used to define the dataset structure
  • Metadata and image importers and processors are used to injest site data into the platform
  • Metadata and image exporters and processors are used to format curated data into a complete dataset

See #project-implementation and #site-implementation for further details.

Getting Started

To get started with SlideTap, follow these steps:

  1. Clone the Repository: 
     git clone https://github.com/your-repo/slidetap.git
 cd slidetap
  2. Set Up Environment Variables: Create a .env file with the necessary environment variables:
     SLIDETAP_CONFIG_FILE=config.yaml
 SLIDETAP_SECRET_KEY=your_secret_key
 SLIDETAP_DBURI=sqlite:///path/to/your/database.db
 SLIDETAP_STORAGE=/path/to/storage
 SLIDETAP_WEBAPP_URL=http://localhost:5000
  3. Install Dependencies: 
     pip install -r requirements.txt
  4. Run the Application: 
     flask run
  5. Run Celery Worker: 
     celery -A slidetap.task.celery worker --loglevel=info

License

SlideTap is licensed under the Apache License, Version 2.0. See the LICENSE file for more details.