Skill: Flow Cytometry Gating Strategist

Recommend optimal flow cytometry gating strategies for given cell types and fluorophores.

Basic Information

• ID: 103
• Name: Flow Cytometry Gating Strategist
• Purpose: Flow cytometry data analysis and gating strategy recommendations

Usage

Command Line

# Recommended format: comma-separated cell types and fluorophores
python scripts/main.py "CD4+ T cells,CD8+ T cells" "FITC,PE,APC"

# Or specify parameters separately
python scripts/main.py --cell-types "CD4+ T cells,CD8+ T cells" --fluorophores "FITC,PE,APC"

# Support more options
python scripts/main.py \
  --cell-types "B cells" \
  --fluorophores "FITC,PE,PerCP-Cy5.5,APC" \
  --instrument "BD FACSCanto II" \
  --purpose "cell sorting"

Parameters

Output Format

{
  "recommended_strategy": {
    "name": "Sequential Gating Strategy",
    "description": "Gating based on FSC-A/SSC-A, followed by fluorescence intensity analysis",
    "steps": [
      {
        "step": 1,
        "gate": "FSC-A vs SSC-A",
        "purpose": "Identify target cell population, exclude debris and dead cells",
        "recommendation": "Set oval gate in lymphocyte region"
      }
    ]
  },
  "fluorophore_recommendations": [
    {
      "fluorophore": "FITC",
      "channel": "BL1",
      "detector": "530/30",
      "considerations": ["May spillover with GFP"]
    }
  ],
  "panel_optimization": {
    "suggestions": ["Recommend pairing weakly expressed antigens with bright fluorophores"],
    "avoid_combinations": ["FITC and GFP used simultaneously"]
  },
  "compensation_notes": ["FITC and PE require careful compensation"],
  "quality_control": ["Recommend setting FMO controls", "Use viability dyes to exclude dead cells"]
}

Supported Cell Types

• T cells: CD4+ T cells, CD8+ T cells, Treg cells, Th1, Th2, Th17, γδ T cells
• B cells: B cells, Plasma cells, Memory B cells, Naive B cells
• Myeloid cells: Monocytes, Macrophages, Dendritic cells, Neutrophils, Eosinophils
• Stem cells: HSC, MSC, iPSC
• Tumor cells: Tumor cells, Cancer stem cells
• Others: NK cells, NKT cells, Platelets, Erythrocytes

Supported Fluorophores