Microendoscope Portal Wiki User Guide¶

Welcome to Microendoscope Portal Wiki! This guide walks you through account setup, data upload, visualization, ROI extraction, and AI-assisted annotation workflows.

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Quick Start¶

Follow these steps to get started:

1. Login & Account Setup
2. Upload Files
3. Convert to SISF Format
4. Scene Viewer
5. Basic Image Adjustments
6. Manage Image Library
7. Annotate ROI with nnInteractive
8. Annotate ROI with Flood Filling

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Tutorials¶

Account & Access¶

• Login
• Forgot Password

Data Preparation¶

• Upload Files
• Convert Files to SISF Format

Visualization & Interaction¶

• Scene Display Window Operations
• Basic Image Adjustments
• Image Library Management

Registration and Stitching¶

• Virtual Stitching
• Chromatic Aberration Correction

Annotation¶

• nnInteractive Annotation Workflow

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Troubleshooting / FAQs¶

• Upload not visible? Check Globus transfer status.
• Seeing black image? Adjust brightness or check conversion.
• nnInteractive login issues? Contact site admin.

If problems persist, please contact the site administrator.

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About¶

This portal supports: - Large-scale multimodal microscopy data - Cloud-enabled storage and streaming - Neuroglancer-based visualization - ROI extraction & AI-assisted annotation via nnInteractive