Beginner Learning Path: Your Journey into Spatial Transcriptomics

Perfect for: New users with no coding experience who want to explore spatial biology through conversation

Total Time Commitment: 4-6 hours over 1-2 weeks
Recommended Pace: 1-2 tutorials per session, with practice time between sessions

Prerequisites Checklist

Before starting this path, ensure you have:

Claude Desktop installed and running
ChatSpatial configured (see Getting Started Guide)
Sample spatial data available (we provide examples)
Basic biology knowledge (cell types, gene expression concepts)
Curiosity and patience - learning through conversation is different!

Learning Objectives

By completing this beginner path, you will:

Master conversational analysis - Learn to ask ChatSpatial the right questions
Understand spatial biology basics - Discover how location matters in tissues
Create beautiful visualizations - Generate publication-ready figures through conversation
Interpret biological results - Make sense of what your analysis reveals
Build confidence - Feel comfortable exploring spatial data independently

Your Learning Journey

Phase 1: Foundation Building (Week 1)

Step 1: Your First Analysis

Tutorial: Basic Spatial Analysis
Time: 90-120 minutes
Difficulty: ⭐☆☆☆☆

What you’ll achieve:

Load your first spatial dataset through conversation
Understand what preprocessing means and why it matters
Discover spatial domains (organized regions) in your tissue
Create your first spatial visualization

Key Conversation Skills:

“Can you load my data at this path?”
“What does preprocessing do and should I do it?”
“Are there organized regions in my tissue?”
“Can you show me a nice visualization?”

Success Indicator: You can confidently load data and identify tissue regions through natural questions.

Step 2: Understanding What’s In Your Tissue

Tutorial: Cell Type Annotation
Time: 60-90 minutes
Difficulty: ⭐⭐☆☆☆

What you’ll achieve:

Discover what types of cells are present in your tissue
Learn about marker genes and how they identify cell types
Validate that cell type assignments make biological sense
Visualize where different cell types are located

Key Conversation Skills:

“What cell types are in my tissue?”
“Can you show me the marker genes for each type?”
“Do these cell type assignments make sense?”
“Where are the different cell types located?”

Success Indicator: You can identify cell types and understand their spatial organization.

Phase 2: Exploring Relationships (Week 1-2)

Step 3: Making Beautiful Pictures

Tutorial: Visualization Tutorial
Time: 45-75 minutes
Difficulty: ⭐⭐☆☆☆

What you’ll achieve:

Create publication-ready figures through simple requests
Customize colors, layouts, and styles conversationally
Generate multiple visualization types for different purposes
Save and export figures for presentations

Key Conversation Skills:

“Can you create a nice plot of my cell types?”
“Make the colors more publication-ready”
“Can you adjust the layout to be cleaner?”
“Save this as a high-resolution figure”

Success Indicator: You can create and customize beautiful visualizations through natural conversation.

Step 4: How Cells Talk to Each Other

Tutorial: Cell Communication Analysis
Time: 75-90 minutes
Difficulty: ⭐⭐⭐☆☆

What you’ll achieve:

Understand how cells send signals to each other
Identify important communication pathways in your tissue
Discover which cells are the main “talkers” and “listeners”
Visualize communication networks spatially

Key Conversation Skills:

“How do my cells communicate with each other?”
“Which pathways are most active?”
“Can you show me the communication network?”
“What does this mean biologically?”

Success Indicator: You can discover and interpret cell communication patterns in your tissue.

Phase 3: Building Confidence (Week 2)

Step 5: Practice and Integration

Time: 60-90 minutes
Difficulty: ⭐⭐⭐☆☆

What you’ll do:

Apply all learned skills to a new dataset
Practice asking follow-up questions based on results
Combine different analysis types in one conversation
Troubleshoot common issues independently

Practice Exercises:

Complete Analysis Flow: Load → Preprocess → Find cell types → Explore communication → Visualize
Question Chain Practice: Ask follow-up questions based on each result
Comparison Analysis: “How does this region differ from that one?”
Biological Interpretation: “What does this tell us about the biology?”

Success Indicator: You can conduct a complete spatial analysis independently through conversation.

What You’ll Achieve

Technical Skills

Conversational Fluency: Ask effective questions to get meaningful results
Data Understanding: Interpret spatial transcriptomics data confidently
Visualization Creation: Generate publication-ready figures
Quality Assessment: Recognize when results make biological sense

Biological Insights

Tissue Organization: Understand how tissues are spatially organized
Cell Type Biology: Identify and validate different cell types
Communication Networks: Discover how cells interact spatially
Pattern Recognition: Spot biologically meaningful patterns

Confidence Building

Independent Analysis: Conduct complete analyses without step-by-step guidance
Question Formulation: Ask progressively more sophisticated questions
Result Interpretation: Make biological sense of computational results
Problem Solving: Handle unexpected results or errors

Time Estimates by Experience

Complete Beginner (No Prior Experience)

Week 1: Steps 1-3 (4-5 hours total)
Week 2: Steps 4-5 (3-4 hours total)
Practice Time: 1-2 hours self-guided exploration

Some Biology Background

Week 1: Steps 1-4 (5-6 hours total)
Week 2: Step 5 + advanced practice (2-3 hours total)

Quick Learners

3-4 focused sessions over 1 week (6-8 hours total)

Success Checkpoints

After Step 2 (Basic + Cell Types)

Can load data through conversation
Understand preprocessing importance
Identify spatial domains confidently
Recognize different cell types
Ask follow-up questions naturally

After Step 4 (Communication)

Interpret cell communication networks
Create customized visualizations
Understand biological significance
Connect spatial patterns to biology
Feel comfortable with the conversation flow

After Step 5 (Complete)

Conduct independent analyses
Ask sophisticated follow-up questions
Troubleshoot issues conversationally
Interpret complex results biologically
Ready for intermediate-level analyses

Common Beginner Questions

“I’m not getting good results - what’s wrong?”

Start with: “Can you check if my data loaded correctly?”
Try: “Are there any quality issues I should address?”
Ask: “What preprocessing steps do you recommend?”

“I don’t understand what this result means”

Ask: “Can you explain what this means biologically?”
Try: “Is this result typical for this tissue type?”
Follow with: “What should I look at next?”

“How do I know if my analysis is correct?”

Request: “Can you validate these results?”
Ask: “Do these cell types make sense for this tissue?”
Check: “Are the spatial patterns biologically plausible?”

Next Steps

Ready for More?

Once you complete this beginner path, consider:

Intermediate Learning Path:

Spatial statistics and pattern analysis
Advanced communication analysis
Multi-sample comparisons
Method selection guidance

Advanced Learning Path:

Trajectory analysis and RNA velocity
Multi-modal integration
Research-level workflows

Stay Engaged

Practice regularly with different datasets
Ask “what if” questions to explore edge cases
Join the community discussions and share results
Read spatial biology papers to build domain knowledge

Ready to begin? Start with Your First Spatial Analysis and remember - every expert was once a beginner!

Questions? The tutorials are designed to be conversational. Just ask ChatSpatial “I’m new to this, can you guide me through the basics?”