CosMx® SMI
Best Practices

Harness the potential of single-cell spatial

We’re unveiling a compilation of expert tips aimed at optimizing your CosMx® SMI spatial runs, ensuring researchers harness the full potential of their instruments effortlessly. Be sure to revisit frequently as we continuously enhance this repository of invaluable best practices.

Volume I: CosMx 1000-plex RNA Assays: Considerations When Generating Single-Cell Spatial Data

• Tip 1: Interpret Data by Tissue and Disease Type
• Tip 2: Consider Sample Preparation Conditions 
• Tip 3: Plan Instrument Run Conditions

Volume II: Tips When Generating Single-Cell Spatial Data: Sample Selection

• Protocol Updates
• Tip 1: Evaluate Tissue Block Quality
• Tip 2: Evaluate Tissue Section Quality
• Tip 3: Consider Tissue Heterogeneity and Autofluorescence

Volume III: Tips when Generating Single-Cell Spatial Data: Post Run H&E and Antibody Staining

• Post-run H&E Staining Protocol
• Post-run Immunofluorescence Staining Protocol

Volume IV: Tips to optimize sample prep for highly autofluorescent samples on CosMx® SMI

• Chemical bleaching during sample preparation
• Benchtop Photobleaching during slide preparation

Volume V: Tips to optimize the CosMx Multiomics sample prep for fragile tissues

• Sequential Readout Workflow Overview 
• The Prevalence of Multiomics Workflow Related Cell Loss 
• How to Assess Multiomics Workflow Related Cell Loss 
• Optimize Sample Preparation for Fragile Tissues 
• General Recommendations 

AtoMx SIP Vol. I: Tips when performing CosMx® data analysis with AtoMx SIP

• Tip 1: Run Quality Control (QC)
• Tip 2: Apply the appropriate normalization 
• Tip 3: Adjust UMAP parameters
• Tip 4: Enhance cell typing results through InSituType
• Tip 5: Refine cell typing clusters
• Tip 6: AtoMx data export enables additional analysis through open-source tools