Set-Up Instructions

Implementation of Glomerular Segmentation model – HistoCloud on HiPerGator:

To enable glomerular segmentation on the powerful HiperGator server, we have prepared a comprehensive documentation that provides step-by-step instructions and best practices. By following this guide, you can leverage the CPU and GPU resources available on HiperGator to achieve highly accurate glomerular segmentations.

Segment WSI tool on Digital Slide Archive:

To access the detailed step-by-step instructions and best practices for segmenting WSIs using HistoCloud’s SegmentWSI tool on Digital Slide Archive, please refer to the provided documentation.

This guide will walk you through the steps, from accessing the Digital Slide Archive to uploading or accessing whole slide images, and then using the SegmentWSI tool for segmentation.

Setting Up Digital Slide Archive

This documentation provides a comprehensive guide for setting up Digital Slide Archive (DSA). It covers the migration process from a previous instance, essential configurations, access restrictions, and system resources. With step-by-step instructions, you’ll learn how to start DSA’s Docker containers, manage rootless Docker configurations, troubleshoot common issues, and enable file transfers. Whether you’re an administrator or developer, this guide equips you with the knowledge to successfully deploy and maintain DSA, ensuring accessibility to your image data and plugins.

Creating a DSA Plugin

Learn how to create custom image analysis plugins for Digital Slide Archive (DSA) in this step-by-step documentation. We’ll show you how to organize your plugin’s files, define input and output parameters, set up the command-line interface (CLI), and deploy Docker images.

Export annotations to Aperio:

The attached documentation offers a comprehensive guide on how to export annotations to Aperio using the Histo-cloud tool. It provides clear, step-by-step instructions for accessing the Digital Slide Archive, uploading or accessing whole slide images, and exporting Aperio XML annotations.

By following the outlined steps, users can easily configure the necessary parameters for the annotation export job. Additionally, the documentation explains how to utilize Aperio (ImageScope Application) to view the annotations.