Nfinder: automatic inference of cell neighborhood in 2D and 3D using nuclear markers.

ABSTRACT:

Background

In tissues and organisms, the coordination of neighboring cells is essential to maintain their properties and functions. Therefore, knowing which cells are adjacent is crucial to understand biological processes that involve physical interactions among them, e.g. cell migration and proliferation. In addition, some signaling pathways, such as Notch or extrinsic apoptosis, are highly dependent on cell-cell communication. While this is straightforward to obtain from membrane images, nuclei labelling is much more ubiquitous for technical reasons. However, there are no automatic and robust methods to find neighboring cells based only on nuclear markers.

Results

In this work, we describe Nfinder, a method to assess the cell's local neighborhood from images with nuclei la

SUBMITTER: Moretti B 

PROVIDER: S-EPMC10239575 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature