Cell Segmentation Performance Assessment (CellSPA) provides an evaluation framework for in situ cell segmentation results.
R package CellSPA can be installed as follows.
BiocManager::install("SydneyBioX/CellSPA")Vignette of CellSPA can be found here: link
If CellSPA has assisted you with your work, please kindly cite our paper:
Fu, X., Lin, Y., Lin, D., Mechtersheimer, D., Wang, C., Ameen, F., Ghazanfar, S., Patrick, E., Kim, J., & Yang, J. Y. H. (2023). Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data. bioRxiv, 2023.2006.2013.544733. https://doi.org/10.1101/2023.06.13.544733