High-plex biomarker imaging with spatial quantification on your FFPE sections.


GeoMX DSP is the first platform to provide high-plex and high-throughput spatial profiling of RNA and protein from a single FFPE section. It enables researchers to identify, spatially map and quantify RNA and protein analytes. The GeoMx DSP utilizes predesigned or custom panels, enabling quantification of up to 96 proteins and over 1,000 RNA molecules on FFPE sections. The tunable region-of-interest selection allows dynamic profiling from complex heterogeneous regions to rare cell specificity. GeoMx DSP provides a comprehensive solution with optimized workflows, off-the-shelf validated assays and integrated data analysis software. Combining Ensigna’s two main areas of expertise, IHC and gene expression analysis, we can now get single cell resolution and digital profiling data for 10’s-1,000’s of RNA or protein analytes.


Here is an example of a bladder cancer section stained with three fluorescent markers: Pan-CK (green),  CD45 (red) and DNA (blue). Masks were applied to delineate the tumor compartment in green/blue (PanCK+) and the stroma in magenta (CD45+). Protein expression was then analyzed independently in these two regions (heat map).



This figure gives you a sense of the capabilities and the new possibilities offered by GeoMX DSP. To learn more about the technology and our services:

• Visit the Nanostring GeoMX DSP website at: https://www.nanostring.com/products/geomx-digital-spatial-profiler/geomx-dsp

• Email us at info@ensigna.com to schedule a free consultation.


Turn your IHC slides into quantitative data.

An important advantage of immunohistochemistry (IHC) is that it maintains the histological structure of a tissue. This allows for the measurement of protein expression in different parts of the tissue down to the cellular and even subcellular level.

Quantifying IHC in each compartment allows one to get additional insight into the biology of the tumor. Epithelial Cell adhesion and Activating Molecule (EpCAM) is a tumor-associated antigen that identifies cells of epithelial origin [1]. EpCAM-based tumor classification is particularly useful when: (a) target marker quantification is required in tumor and stromal regions (b) target marker is absent in tumor cells but present in stromal compartment; (c) target marker is expressed only in tumor cells and background staining is seen in the stroma.

Staining serial sections with EpCAM and a marker of interest allows us to use the HALO® software from Indica Labs to quantify the IHC staining in the tumor compartment and the surrounding stroma independently. 

EpCAM Staining to Identify Tumor Compartment 

The software is trained to recognize EpCAM positive staining by manually identifying regions that are positive, negative or contain no tissue (glass) as shown by red, green and yellow arrows, respectively, in Figure 1B. Based on the experimenter’s input (Figure 1B), the algorithm is then able to classify the entire image into three categories: EpCAM positive, EpCAM negative and glass as shown in Figure 1C. 

Figure 1: EpCAM Staining to Identify the Tumor Compartment

Quantification of Target Marker using EpCAM Staining 

We apply a series of steps to overlay the classified regions from EpCAM staining onto target markers (Marker B in Figure 2) using serial sections that were stained for EpCAM and Marker B. The following steps outline the entire process.

Figure 2: Quantification of Marker B by result from EpCAM Staining 

Step 1: Create a classifier based on EpCAM positivity as defined in EpCAM Staining. 

  • Red: Tumor
  • Green: Strom
  • Yellow: Glass

Step 2: Create an annotation (red outline) for the tumor compartment based on the EpCAM classifier.

Step 3: Copy annotation onto Marker B image.

Step 4: Analyze Marker B IHC only in the tumor annotation.

This approach allows for the quantification of markers that are differently modulated in the tumor versus the stromal compartment. This is another example of how we at Ensigna Biosystems use cutting edge methods to help our clients answer scientific questions relevant to their drug discovery projects.


  1. Okegawa T, Pong RC, Li Y, Hsieh JT. The role of cell adhesion molecule in cancer progression and its application in cancer therapy. Acta Biochim Pol. 2004;51(2):445-457.


We are proud to announce that Ensigna Biosystems is expanding and has moved to the Gate510 Tech Campus in San Leandro. To accommodate our rapid growth, the brand new space comprises of 5,300 more square feet of office and lab space than our previous location in Richmond.

With this larger space, we are able to provide our clients with more histopathology and molecular biology services, fully equipped with a cell culture facility, Leica Bond, nanoString, GeoMX DSP, Huron and Aperio scanners, LiCor Odyssey Imaging System. 

This expansion represents a new phase for the company, its employees and its clients. It symbolizes Ensigna’s achievements and thriving business since its founding in 2014. Our new facility will offer us the opportunity to better serve our loyal clients and work with our valuable business partners. We are very excited to share the news and look forward to continuing to serve your needs and work with you at our new location in the coming years. 


Please update your records with our new address:

1933 Davis Street

Suite 200

San Leandro, CA 94577


Our phone numbers and email addresses have remained the same: 

Tel: 510-860-4445

Fax: 510-984-2157