Cell Spatial Analysis in Crohn's Disease: Unveiling Local Cell
  Arrangement Pattern with Graph-based Signatures
Shunxing Bao Sichen Zhu Vasantha L Kolachala Lucas W. Remedios Yeonjoo Hwang Yutong Sun Ruining Deng Can Cui Yike Li Jia Li Joseph T. Roland Qi Liu Ken S. Lau Subra Kugathasan Peng Qiu Keith T. Wilson Lori A. Coburn Bennett A. Landman Yuankai Huo
Crohn's disease (CD) is a chronic and relapsing inflammatory condition that
affects segments of the gastrointestinal tract. CD activity is determined by
histological findings, particularly the density of neutrophils observed on
Hematoxylin and Eosin stains (H&E) imaging. However, understanding the broader
morphometry and local cell arrangement beyond cell counting and tissue
morphology remains challenging. To address this, we characterize six distinct
cell types from H&E images and develop a novel approach for the local spatial
signature of each cell. Specifically, we create a 10-cell neighborhood matrix,
representing neighboring cell arrangements for each individual cell. Utilizing
t-SNE for non-linear spatial projection in scatter-plot and Kernel Density
Estimation contour-plot formats, our study examines patterns of differences in
the cellular environment associated with the odds ratio of spatial patterns
between active CD and control groups. This analysis is based on data collected
at the two research institutes. The findings reveal heterogeneous
nearest-neighbor patterns, signifying distinct tendencies of cell clustering,
with a particular focus on the rectum region. These variations underscore the
impact of data heterogeneity on cell spatial arrangements in CD patients.
Moreover, the spatial distribution disparities between the two research sites
highlight the significance of collaborative efforts among healthcare
organizations. All research analysis pipeline tools are available at
https://github.com/MASILab/cellNN.