Single-Molecule RNAscope / FISH
Counts individual transcript puncta per cell to quantify gene expression at single-molecule resolution.
- Ch1: DAPI
- Ch2-4: RNAscope/FISH probe channels (one per target gene)
- Spot count per cell per channel
- Spot intensity
- % cells expressing each transcript
Everything you need for single-molecule rnascope / fish
Automated, reproducible, and code-free analysis in the cloud
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Fully automated
Upload your images and get publication-ready results. No coding or scripting needed.
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How it runs
Cytely automates the image analysis so you can focus on the science.
Segment nuclei from DAPI
Detect puncta per probe channel
Count and measure per cell.
Compatibility
Supported
Single-probe and multiplex (up to 4 channels), nuclear vs cytoplasmic transcript localization.
Not yet supported
Transcript co-localization at single-spot resolution, 3D spot detection in Z-stacks, spatial transcriptomics grid analysis.
1 Dependent on sample quality
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