QuPath RNA ISH Analysis
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”
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.
