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Digital Pathology Image Analysis

To accurately interpret gene expression in tissues, scientists are in need of a quantitative assay that provides spatial information at the molecular level. The RNAscope™, BaseScope™, and miRNAscope™ ISH technologies enable single molecule detection of RNAs in situ within the tissue context. Our highly trained scientific experts and pathologists offer various quantification methodologies. The analyses are defined according to the biological question being addressed, and each project is supported by consultations with the scientific team.

Digital Image Analysis

• Quantitative cell-by-cell gene expression data

• Identify tissue types or regions of interest

• Optional heat maps provide full-tissue spatial expression


Image analysis is performed using HALO™ (Indica Labs), the powerful digital pathology tool for quantitative gene expression analysis. HALO reports morphological and multiplexed gene expression data on a cell-by-cell basis across entire tissue sections, and is applicable for RNAscope, BaseScope, and miRNAscope singleplex, duplex, and multiplex fluorescence assays. Sorting and filtering capabilities allow the user to mine millions of cells while visually assessing the corresponding cells in situ. The software can be trained to classify cell populations or regions of interest (ROI), for example categorizing a tissue into tumor cells versus stromal cells.  


Heterozygous expression of EGFR in human breast cancer tissue. RNAscope staining (left) and HALO image analysis markup (right), showing cells binned according to level of gene expression based on dots per cell

Example of HALO analysis of  NSCLC tissue stained with the RNAscope Duplex assay for CD45 (red) and PD-L1 (green). Co-expressing cells shown in yellow




• In-house pathologists for image annotations

• Histopathology notes include tumor load and visual H-scoring

• Teleconference with pathologists for data presentation and review

Your pathologist’s workload can be reduced by utilizing our team’s in-house and contract pathologists who will provide additional notations or review for any study. Annotations can be performed manually either to identify regions of inclusion or regions of exclusion, for instance to exclude regions of necrosis or poor positive control staining. Visual H-scoring can also be performed by a pathologist to provide more quantitative results (see manually annotated regions of interest in tumor tissue sample by our pathologist below).


Tumor compartment only

Tumor-associated stroma

Tumor and tumor-associated stroma


Semi-Quantitative Visual Scoring

•Semi-quantitative scoring performed by highly trained experts

•Rapid scoring shortens turnaround time and speeds delivery of results

•Provides expression level and percentage of cells positive

For gene expression studies where understanding relative signal intensity is sufficient, visual semi-quantitative scoring can be used to provide a single score based on the expression level observed. RNAscope ISH staining generates punctate chromogenic or fluorescent signals. Scoring is based on counting the number of dots per cell, with each dot corresponding to a single RNA molecule. Visual scoring (0–4) is performed based on the predominant staining pattern seen throughout the entire sample or within a defined region of interest. Heterogeneity or non-uniformity of expression will be noted. Percentage of cells positive is scored visually based on number of cells with ≥1 dot/cell and binned into categories (i.e., 0%, 1–25%, 26–50%, 51–75, 76–99%, 100%).

                Scores (0–4) are assigned to a tissue sample based on the number of dots/cell

Download Image Analysis Flyer

Download Image Analysis Flyer

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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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