Tumor Area Quantification

Tumor Area Quantification2022-07-12T14:08:53-05:00


The microscopic examination of tissue morphology using Hematoxylin and Eosin (H&E) is the standard practice in histopathology for visual analysis of tissue specimens. One of the most common features for which pathologists evaluate H&E images is overall percent tumor area. This is important not only to the ultimate diagnosis of cancer, but also to prognostic outcomes, and to demarcating what image regions of interest should be considered for future analysis of other biologically relevant markers such as angiogenesis, immune cell infiltration, or over expression of cancer-specific proteins like HER2 or BRCA1/2 in the case of breast cancer.


Figure 1. Example of tumor area fraction in breast cancer lumpectomy tissue biopsy H&E image, determined using a machine learning approach. The outlined tumor area is highlighted in red superimposed on the original image. Drag the slider to switch between images before and after segmentation.


InstrumentAperio XT2 Slide Scanner
Analysis MethodBrightfield Imaging
MarkersHematoxylin and Eosin (H&E)
Sample SubmissionWhole Tissue fixed and stored in PBS with 0.05% azide
Formalin Fixed Paraffin Embedded (FFPE) tissue blocks
Tissues embedded in OCT
Pre-stained and mounted slides
Digitized slide images
Imaging Parameters20X, 40X magnification
Image Analysis Cell counting
Tumor area quantification
Analysis of Nuclear Morphology
Data DeliveryWhole Slide Images in RGB format, ROI masks (e.g. tumor vs. non-tumor regions), data tables containing cell counts

General Procedure

  1. Tissue sample is transferred to Visikol in PBS w/ 0.05% azide or in a form most appropriate for the customer (e.g. FFPE, OCT compound).
  2. Alternatively, mounted and stained slides or digitized images of H&E slides can be sent for analysis.
  3. The sample is processed, sectioned, and stained with Hematoxylin and Eosin.
  4. The sample slides are imaged with high-throughput slide scanner at desired magnification.
  5. The images are then processed and analyzed according to customer specifications.
  6. Images and quantification report are then transferred to the customer.


  1. Feldman, A.T., Wolfe, D. (June 2014). “Tissue Processing and Hematoxylin and Eosin Staining”. Histopathology. pp. 31-43.