Skip to contents

The seqFISH technology enables in situ profiling of individual molecules such as RNA, DNA, and protein via sequential rounds of fluorescent labeling and imaging (Lubeck, et. al.). The sequential labeling and imaging rounds can identify up to 24,000 unique targets, and recent publications have demonstrated the ability of the technology to robustly detect 10,000 genes in individual cells (Eng, et. al.). To date, seqFISH has been applied to a number of tissue and organisms, including brain, mouse embryo, and zebrafish embryo.

Pros and cons


  • Single cell resolution
  • High detection efficiency
  • Commercial kit coming
  • Get subcellular transcript localization information
  • Compatible with histological features such as DAPI and membrane staining


  • Need to pre-select a panel of usually a few hundred genes

Analysis Workflows

The analysis tasks include basic quality control, spatial exploratory data analysis, identification of spatially variable genes, and computation of global and local spatial statistics. Accompanying Colab notebooks are linked when available.

Vignette Colab Notebook Description
seqFISH exploratory data analysis Colab Notebook Perform basic QC, data normalization, dimension reduction, clustering, univariate spatial statistics, significance testing