HiTMicTools

User Guide

  • Launching the Analysis Pipeline
    • Overview
    • 1. Prerequisites
      • Environment Setup
      • Installation
      • Dependency Note
      • Required Assets
    • 2. Project Structure
    • 3. Configuration File
      • Basic Configuration Example
      • Configuration Parameters Explained
      • Available Pipelines
      • Processing Single Files
    • 4. Running the Analysis
      • Basic Command
      • Using a Worklist
      • CLI Help
    • 5. Understanding the Output
      • Output Files
      • CSV Output Columns
    • 6. Monitoring and Performance
      • Parallel Processing
      • Resource Usage Tips
      • Progress Monitoring
    • 7. Troubleshooting
      • Common Issues
      • Getting Help
    • 8. Advanced Configuration
      • Using Individual Models (Alternative to Model Collections)
  • Launching Analysis with Cell Tracking
    • Overview
    • About btrack
    • 1. Prerequisites
      • btrack Installation
      • Model Collection with Tracking Support
    • 2. Understanding Tracking Configuration
      • Tracking Configuration Structure
      • Default Configuration Example
      • Critical Parameters for Tuning
    • 3. Pipeline Configuration
      • Basic Tracking Setup
      • Custom Tracking Parameters
      • Using a Custom Tracking Config File
    • 4. Running Analysis with Tracking
      • Command
      • Expected Output
      • Processing Notes
    • 5. Understanding Tracking Output
      • Output Files
      • Tracking Columns in CSV
      • Lineage Relationships
    • 6. Validating Tracking Results
      • Visual Validation
      • Diagnostic Metrics
    • 7. Optimizing Tracking Parameters
      • Workflow for Parameter Tuning
      • Parameter Adjustment Guide
      • Example Optimized Config
    • 8. Troubleshooting
      • Common Issues
      • Performance Tips
    • 9. Advanced Tracking Features
      • Region of Interest (ROI) Constraints
      • Update Methods
      • Custom Features
    • 10. Downstream Analysis
      • Loading Tracking Data
      • Visualization
      • Export for External Tools
    • Summary
  • Using SLURM for Large-Scale Analysis
    • Overview
    • Workflow Summary
    • 1. Prerequisites
      • Cluster Access
      • Environment Setup on Cluster
      • File Organization
    • 2. Splitting Files into Batches
      • Basic Usage
      • Advanced Options
      • Determining Block Count
    • 3. Generating SLURM Scripts
      • Basic Command
      • All Available Options
      • Understanding the Generated Script
    • 4. Customizing SLURM Scripts
      • Adjusting Resource Requests
      • Understanding Partitions and QoS (Quality of Service)
      • Modifying Array Size
      • Email Notifications
    • 5. Submitting and Managing Jobs
      • Submitting Jobs
      • Monitoring Jobs
      • Queue Status Output
      • Canceling Jobs
      • Checking Resource Usage
    • 6. Configuration for SLURM
      • Adapting Your Config File
      • Testing Configuration
    • 7. Best Practices
      • Resource Optimization
      • Data Management
      • Error Handling
    • 8. Example Workflows
      • Workflow 1: Standard Analysis (100 files)
      • Workflow 2: Large-Scale Tracking (500 files)
      • Workflow 3: Reprocessing Subset
    • 9. Troubleshooting
      • Job Pending Forever
      • Out of Memory Errors
      • GPU Not Available
      • Files Not Found
    • 10. Advanced Topics
      • Dependency Chains
      • Checkpoint and Resume
      • Custom SLURM Directives
    • Summary
  • Model Management and Resource Control
    • Overview
    • 1. Model Collections (Recommended Approach)
      • Advantages of Model Collections
      • Available Model Collections
      • Using Model Collections
      • Creating Custom Model Collections
    • 2. Individual Model Specification (Advanced)
      • Complete Individual Model Configuration
      • Model Loading Details
    • 3. Model Architectures
      • Focus Restoration Models
      • Segmentation Models
      • Classification Models
    • 4. Resource Management
      • The ReserveResource System
      • How It Works
      • Configuration for Multi-Process
      • Memory Logging
      • Cleanup and Cache Management
    • 5. Model Performance and Optimization
      • Inference Speed Optimization
      • Typical Performance Metrics
      • Model Versioning and Reproducibility
    • 6. Troubleshooting Models
      • Model Loading Errors
      • Model Performance Issues
    • 7. Model Storage Best Practices
      • File Organization
      • Version Control
      • Model Distribution
    • Summary
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