Welcome to VASCilia’s documentation!

Contents:

• Overview
  • VASCilia: Vision Analysis StereoCilia
  • Pipeline Overview
  • Features
  • Applications
  • Getting Started
• Installation
  • Requirements
  • Steps
• Set Up WSL
• STEP 2: Download the Deep Learning Trained Models
• STEP 3: Download a Test Dataset
• Instructions for Cloning and Installing the Repository
  • Option A: Cloning the Repository
  • Option B: Installing via PyPI
• Multi-Batch Processing Feature: Required File
  • Download the File
  • Instructions
• Quick Start: Demo Datasets and Tutorials
  • Demo Datasets
  • Tutorial Videos
• Open Image
  • Key Features
  • Differences in File Handling
  • Summary of File Handling
  • Handling Padding and Resizing
  • Usage Instructions
  • Extending the Functionality
• Trim Cochlea Stacks
  • Key Features
  • Example Workflow
• Trim AI Prediction: Automatic Start and End Index Selection
  • Key Components
  • Workflow and Usage
  • Practical Considerations
  • Extending the Functionality
• Rotate Cochlea Stacks
  • Key Features
• AI Prediction: Automatic Rotation Angle Selection
  • Key Components
  • Workflow and Usage
  • Practical Considerations
  • Extending Rotation Functionality
  • Extending the Functionality
• 3D Segmentation of Cochlea Stacks
  • Key Features
  • Usage Instructions
  • Technical Details
  • Why Segmentation is Important
  • Practical Considerations
  • Extending the Functionality
• Visualizing and Tracking Cochlea Segmentations
  • Key Features
  • Why Visualization and Tracking Are Important
  • Batch Processing with SORT Algorithm
  • Usage Instructions
  • Technical Details
  • Practical Considerations
  • Extending the Functionality
• Deleting Labels in Cochlea Segmentations
  • Key Features
  • Usage Instructions
  • Extending the Functionality
• Calculating Measurements for Labeled Volumes
  • Key Features
  • Usage Instructions
  • Practical Considerations
  • Example Workflow
  • Extending the Functionality
• Calculating and Saving length for Bundle Heights
  • Key Features
  • Usage Instructions
  • Example Workflow
  • Extending the Functionality
• Cell Clustering
  • Key Features
  • Workflow
  • Practical Considerations
  • Directory Structure
  • Usage Instructions
  • Output Examples
  • Extending the Functionality
• Signal Computation
  • Key Functionalities
  • Workflow
  • Directory Structure
  • Usage Instructions
  • Practical Considerations
  • Output Examples
  • Extending the Functionality
• Region Prediction
  • Key Features
  • Usage Instructions
  • Model Details
  • Example Output
  • Practical Considerations
  • Extending the Functionality
• Orientation Computation
  • Key Features
  • Usage Instructions
  • Example Workflow
  • Practical Considerations
  • Outputs
  • Extending the Functionality
• Batch Processing
  • Key Features
  • Single-Stack Workflow
  • Multi-Stack Workflow
  • Example Workflow
  • Practical Considerations
  • Extending the Functionality
• Upload Previously Processed Cochlea Data
  • Overview
  • Usage Instructions
  • Features
  • Error Handling
  • Advanced Features
  • Notes
  • Extending the Functionality
• Commuting Training Action
  • Features
  • Error Handling
  • File Management
  • Extending the Functionality
• Reset or Exit VASCilia
  • Extending the Functionality

Indices and tables

• Index

• Module Index

• Search Page