QuPath RNA ISH Analysis

QuPath, short for Quantitative Pathology, is an open-source software that provides automated quantitative and semi-quantitative analysis of whole slide images. By using the built-in algorithms, QuPath offers a complete workflow for spatial RNA analysis - starting from color deconvolution, through stages of cell detection, subcellular probe identification, and classification, all the way to the final cell-by-cell RNA quantification.


QuPath RNA ISH / FISH Analysis Features:

  • Free open-source platform*
  • Analysis of Single, Duplex, Multiplex, or Higher Plexing experiments
  • Detection of individual and clustered RNA dots
  • Subcellular dot-count-based and optical-density-based quantification
  • Visualization of classification results
  • Tabulated and graphical statistical outputs
  • Scriptable workflow for batch processing

Tech Note

Download our Tech Note for “Using QuPath to analyze RNAscope™, BaseScope™ and miRNAscope™ images”

Download pdf


QuPath is compatible with the following RNAscope, BaseScope, and miRNAscope Assays:

RNAscope Assays

BaseScope Assays

miRNAscope Assays

RNAscope™ 2.5 HD Reagent Kit—BROWN

RNAscope™ 2.5 HD Reagent Kit—RED

RNAscope™ 2.5 HD Duplex Reagent Kit

RNAscope™ Fluorescent Multiplex Reagent Kit

RNAscope™ Multiplex Fluorescent Reagent Kit v2

RNAscope HiPlex12 Reagents Kit (488, 550, 647)

RNAscope HiPlex12 Reagents Kit (488, 550, 647, 750)

RNAscope™ LS Reagent Kit—BROWN

RNAscope™ LS Reagent Kit—RED

RNAscope™ LS Multiplex Fluorescent Reagent Kit

RNAscope™ VS Universal AP Reagent Kit

RNAscope™ VS Universal HRP Reagent Kit

RNAscope™ VS Duplex Reagent Kit

RNAscope™ 2.5 LS Duplex Reagent Kit-(RED/BROWN)

BaseScope™ Reagent Kit v2 – RED

BaseScope™ Duplex Reagent Kit

BaseScope™ VS Reagent Kit

BaseScope™ LS Reagent Kit


miRNAscope™ HD Reagent Kit – RED

miRNAscope™ LS Reagent Kit - RED




QuPath guidelines provided are For Research Use Only. Not For Use In Diagnostic Procedures.

QuPath is an open-source software that provides automated quantitative and semi-quantitative analysis of whole slide images. Visit QuPath’s website for more information: https://qupath.readthedocs.io/en/latest/.


* Download, use or access of this open-source software is voluntary, at your own risk and governed by QuPath’s terms and conditions. If you choose to download, access or use this open-source software, confirm beforehand that any of these actions comply with your organization’s internet, information security, privacy, technology and other applicable company policies. ACD and its affiliates assume no, and specifically disclaim any and all, liability for any damages associated with such use or access.

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