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 FastAPI 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

See tasks for more information.

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 site implementations and dataset implementations for further details.

Example application

For an ready-made example application, see example.

License

SlideTap: Copyright 2024 Sectra AB, licensed under Apache 2.0.

Acknowledgement

This project is part of a project that has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 945358. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA. IMI website: