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Software solutions for all your research needs

The single-molecule sensitivity and visualization makes quantitative RNA in situ hybridization analysis a cutting edge solution. Although many labs do evaluate target probe signals manually using scoring guidelines, the tasks are time consuming and prone to subjectivity and poor reproducibility. Advanced Cell Diagnostics have partnered with Definiens, Indica Lab and Leica Biosystems to facilitate and improve quantitative scoring. These advanced image analysis solution brings objective and accurate quantification to RNA in situ hybridization. For the first time, gene expression can be measured quantitatively and interpreted by research pathologists within histopathological context.

You can select from Halo Software from Indica Lab or Aperio RNA ISH Algorithm by Leica Biosystems for automated image analysis solutions for RNAscope® Assays.

RNAscope® In Situ Hybridization Assay Workflow

  • Step 1:


    Tissue sections or cells are fixed onto slides and pretreated with RNAscope® Pretreatment Kit to unmask target RNA and permeabilize cells.

  • Step 2:


    Designed with ~20 target-specific double Z probes, RNAscope® Probes hybridize to target RNA molecules.

  • Step 3:


    RNAscope® Detection Reagents amplify the hybridization signals via sequential hybridization of amplifiers and label probes.

  • Step 4:


    Each punctate dot signal represents a single test target RNA molecule and can be visualized with a microscope.

  • Step 5:


    Single-molecule signals can be quantified on a cell-by-cell basis by manual counting or automated image analysis using HALO Software.

Which Software is right for me?

Aperio RNA ISH Algorithm

HALO Software


Aperio RNA ISH Algorithm by Leica Biosystems

Indica Lab


Quantitative and semi-quantitative outputs Singleplex, brightfield quantification Duplex, brightfield quantification- Red/Green Count individual cells or clusters Identify subcellular location of signal (nucleus, cytoplasm) Compatible with full Aperio Digital Pathology solution

Quantitative and reproducible RNAScope spot counting Singleplex, brightfield quantification Multiplex, brightfield quantification Multiplex, fluorescent ISH quantification Cell-by-cell expression profiles High throughput computing power for faster turnaround time Whole-slide image or field-of-view image analysis Manual and automatic selection of distinct cell populations Easy to use and learn

Assay Compatibility

RNAscope® 2.5 HD Reagent Kit—BROWN RNAscope® 2.5 HD Reagent Kit—RED RNAscope® 2.5 HD Duplex Reagent Kit RNAscope® 2.5 LS Reagent Kit—BROWN RNAscope® 2.5 LS Reagent Kit—RED RNAscope® 2.5 VS Reagent Kit—BROWN RNAscope® 2.5 VS Reagent Kit—RED

RNAscope® 2.5 HD Reagent Kit—BROWN RNAscope® 2.5 HD Reagent Kit—RED RNAscope® 2.5 HD Duplex Reagent Kit RNAscope® Multiplex Fluorescent Reagent Kit RNAscope® 2.5 LS Reagent Kit—BROWN RNAscope® 2.5 LS Reagent Kit—RED RNAscope® 2.5 VS Reagent Kit—BROWN RNAscope® 2.5 VS Reagent Kit—RED

ACD Pharma Assay Services

Image analysis service available

Image analysis service available

Commercial Availability

Available for purchase from Leica Biosystems

Available for purchase from Indica Lab

License Type

One-time license

Annual single or network licenses

Aperio RNA ISH Algorithm is: For Research Use Only. Not For Use In Diagnostic Procedures.

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Advanced Cell Diagnostics

Our new headquarters office starting May 2016:

7707 Gateway Blvd.  
Newark, CA 94560
Toll Free: 1 (877) 576-3636
Phone: (510) 576-8800
Fax: (510) 576-8798



19 Barton Lane  
Abingdon Science Park
OX14 3NB
United Kingdom
Phone 2: +44 1235 529449
Fax: +44 1235 533420



Advanced Cell Diagnostics China

Building 15, No. 26 Xihuan South Road
Beijing Economic-Technological Development Area
Beijing, China, Zip code: 100176

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