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
HiTMicTools
Index
Index