ESQmodel: biologically informed evaluation of 2-D cell segmentation quality in multiplexed tissue images.
Bioinformatics
; 40(1)2024 01 02.
Article
in En
| MEDLINE
| ID: mdl-38152895
ABSTRACT
MOTIVATION Single cell segmentation is critical in the processing of spatial omics data to accurately perform cell type identification and analyze spatial expression patterns. Segmentation methods often rely on semi-supervised annotation or labeled training data which are highly dependent on user expertise. To ensure the quality of segmentation, current evaluation strategies quantify accuracy by assessing cellular masks or through iterative inspection by pathologists. While these strategies each address either the statistical or biological aspects of segmentation, there lacks a unified approach to evaluating segmentation accuracy. RESULTS:
In this article, we present ESQmodel, a Bayesian probabilistic method to evaluate single cell segmentation using expression data. By using the extracted cellular data from segmentation and a prior belief of cellular composition as input, ESQmodel computes per cell entropy to assess segmentation quality by how consistent cellular expression profiles match with cell type expectations. AVAILABILITY AND IMPLEMENTATION Source code is available on Github at https//github.com/Roth-Lab/ESQmodel.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Software
/
Somatostatin-Secreting Cells
Language:
En
Journal:
Bioinformatics
Year:
2024
Document type:
Article