Intest Res.  2019 Jul;17(3):387-397. 10.5217/ir.2018.00167.

Quantitative histology-based classification system for assessment of the intestinal mucosal histological changes in patients with celiac disease

  • 1Department of Pathology, All India Institute of Medical Sciences, New Delhi, India.
  • 2Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, India.
  • 3Department of Biostatistics, All India Institute of Medical Sciences, New Delhi, India.


The existing histological classifications for the interpretation of small intestinal biopsies are based on qualitative parameters with high intraobserver and interobserver variations. We have developed and propose a quantitative histological classification system for the assessment of intestinal mucosal biopsies.
We performed a computer-assisted quantitative histological assessment of digital images of duodenal biopsies from 137 controls and 124 patients with celiac disease (CeD) (derivation cohort). From the receiver-operating curve analysis, followed by multivariate and logistic regression analyses, we identified parameters for differentiating control biopsies from those of the patients with CeD. We repeated the quantitative histological analysis in a validation cohort (105 controls and 120 patients with CeD). On the basis of the results, we propose a quantitative histological classification system. The new classification was compared with the existing histological classifications for interobserver and intraobserver agreements by a group of qualified pathologists.
Among the histological parameters, intraepithelial lymphocyte count of ≥25/100 epithelial cells, adjusted villous height fold change of ≤0.7, and crypt depth-to-villous height ratio of ≥0.5 showed good discriminative power between the mucosal biopsies from the patients with CeD and those from the controls, with 90.3% sensitivity, 93.5% specificity, and 96.2% area under the curve. Among the existing histological classifications, our quantitative histological classification showed the highest intraobserver (69.7%-85.03%) and interobserver (24.6%-71.5%) agreements.
Quantitative assessment increases the reliability of the histological assessment of mucosal biopsies in patients with CeD. Such a classification system may be used for clinical trials in patients with CeD.


Celiac disease; Intestine, small; Morphometry; Image analysis; Histology, quantitative

MeSH Terms

Celiac Disease*
Cohort Studies
Epithelial Cells
Intestine, Small
Logistic Models
Lymphocyte Count
Observer Variation
Sensitivity and Specificity


  • Fig. 1. (A) Showing receiver operating characteristic (ROC) considering pathological cutoff of the IEL count ≥25/100 ECs for differentiating duodenal biopsies from patients with celiac disease and controls, with area under the ROC (AUC) of 93.7% (95% CI, 91.1%–96.1%). (B) ROC considering pathological cutoff of Vh <335 µm, with AUC 96.4% (95% CI, 94.3%–98.5%). (C) ROC considering the pathological cutoff for Cd:Vh ratio ≥0.66, with AUC 88.2% (95% CI, 84.1%–92.3%). (D) ROC considering villous area cutoff at ≥750 µm2 , with AUC 65.6% (95% CI, 58.8%–72.4%). IEL, intraepithelial lymphocytes; ECs, epithelial cells; Vh, villous height; Cd, crypt depth.

  • Fig. 2. (A) Photomicrograph shows a villous tip with increased intraepithelial lymphocytes (IELs; arrows) (H&E, ×200). (B) The method of manual tagging of anti-CD3 positive IELs by using the computer assisted image analysis-based software mentioned (immunostaining, ×100). (C) The method of measuring the mucosal epithelial heights at the villous tips (H&E, ×400). (D) Method of measuring the Cd:Vh and the villous areas (H&E, ×10). (E) A duodenal biopsy with increased IELs and Cd:Vh >0.5, hence, categorized as type 2 changes (H&E, ×100). (F) IEL count ≥25/100 ECs, Vh fold change ≤0.7 and Cd:Vh ratio ≥0.5, hence, categorized as type 3 changes (H&E, ×100). The black lines in the D-F are representing the imaginary shoulder of these biopsy fragments. Cd, crypt depth; Vh, villous height; ECs, epithelial cells.


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