ST-CellSeg: Cell segmentation for imaging-based spatial transcriptomics using multi-scale manifold learning.
PLoS Comput Biol
; 20(6): e1012254, 2024 Jun.
Article
em En
| MEDLINE
| ID: mdl-38935799
ABSTRACT
Spatial transcriptomics has gained popularity over the past decade due to its ability to evaluate transcriptome data while preserving spatial information. Cell segmentation is a crucial step in spatial transcriptomic analysis, as it enables the avoidance of unpredictable tissue disentanglement steps. Although high-quality cell segmentation algorithms can aid in the extraction of valuable data, traditional methods are frequently non-spatial, do not account for spatial information efficiently, and perform poorly when confronted with the problem of spatial transcriptome cell segmentation with varying shapes. In this study, we propose ST-CellSeg, an image-based machine learning method for spatial transcriptomics that uses manifold for cell segmentation and is novel in its consideration of multi-scale information. We first construct a fully connected graph which acts as a spatial transcriptomic manifold. Using multi-scale data, we then determine the low-dimensional spatial probability distribution representation for cell segmentation. Using the adjusted Rand index (ARI), normalized mutual information (NMI), and Silhouette coefficient (SC) as model performance measures, the proposed algorithm significantly outperforms baseline models in selected datasets and is efficient in computational complexity.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Algoritmos
/
Biologia Computacional
/
Perfilação da Expressão Gênica
/
Transcriptoma
/
Aprendizado de Máquina
Limite:
Humans
Idioma:
En
Ano de publicação:
2024
Tipo de documento:
Article