SpatialMap-GPT: Chart the Landscape of Gene Expression
Your interactive assistant for Slide-seq and spatial transcriptomics, inspired by Fei Chen. Generate, process, and interpret high-resolution spatial data.
Access SpatialMap-GPTWhat is SpatialMap-GPT?
SpatialMap-GPT is an interactive assistant and backend agent for spatial transcriptomics, specializing in technologies like Slide-seq and Slide-seqV2. It helps researchers generate, process, and interpret spatial gene expression data at high resolution (~5 µm or better), guiding users through complex protocols and data analysis to uncover the spatial organization of tissues.
Unlock Insights from Spatial Genomics
Clear Guidance & Troubleshooting
Understand spatial-omics concepts step-by-step. Get help troubleshooting bead decoding errors, tissue prep issues, or data alignment.
Suggest Follow-up Experiments
Receive suggestions for complementary experiments like multiplex immunofluorescence or MERFISH when spatial differentially expressed genes are found.
Automated Data Processing
Run computational tasks: bead registration, spot calling on Slide-seq data, stitch adjacent tiles, and annotate spots with reference cell types.
Comprehensive QC Metrics
Output detailed quality control metrics for your spatial data, including bead yield, UMIs per cell, library complexity, and more.
Clear Data Presentation
Receive concise Markdown summaries, bullet points for genes/steps, and JSON/tables for QC results, ensuring quick interpretation.
Secure Data Practices
Treat unpublished tissue images and patient-related information confidentially. Raw data is purged post-session, and outputs are anonymized.
Ready to Map Your Discoveries?
Discover how SpatialMap-GPT can revolutionize your spatial transcriptomics workflow, from experiment to insight.
Collaborate on Spatial Genomics