SpaTopic: Spatial Topic Modeling for Multiplexed Images

SpaTopic is a package for spatial topic modeling of Multiplexed images. It adapts an approach originally developed for image segmentation in computer vision, incorporating spatial information into the flexible design of regions (image partitions, analogous to documents in language modeling). We further refined the approach to address unique challenges in cellular images and provide an efficient C++ implementation of the algorithm in this R package.

Compared to other KNN-based methods (such as KNN-kmeans, the default neighborhood analysis in Seurat v5 R package), SpaTopic runs much faster on large-scale image datasets.

The main functions in the 'SpaTopic' package

• Prepare input Seurat5obj_to_SpaTopic

• Model Inference SpaTopic_inference

• Print results print.SpaTopic

Source

<https://github.com/xiyupeng/SpaTopic>

See also

Useful links:

• https://github.com/xiyupeng/SpaTopic

• Report bugs at https://github.com/xiyupeng/SpaTopic/issues

Author

Xiyu Peng pansypeng124@gmail.com