Published September 11, 2023 | Version v1.0.0
Software Open


  • 1. Xidian University
  • 2. University of Pennsylvania
  • 3. Children's Hospital of Philadelphia


It remains poorly understood how different cell phenotypes organize and coordinate with each other to support tissue functions. To better understand the structure-function relationship of a tissue, the concept of tissue cellular neighborhoods (TCNs) has been proposed. Furthermore, given a set of tissue images associated with different conditions, it is often desirable to identify condition-specific TCNs with more biological and clinical relevance. However, there is a lack of computational tools for de novo identification of condition-specific TCNs by explicitly utilizing tissue image labels.

We developed the CytoCommunity algorithm for identifying TCNs that can be applied in either an unsupervised or a supervised learning framework. The direct usage of cell phenotypes as initial features to learn TCNs makes it applicable to both single-cell transcriptomics and proteomics data, with the interpretation of TCN functions facilitated as well. Additionally, CytoCommunity can not only infer TCNs for individual images but also identify condition-specific TCNs for a set of images by leveraging graph pooling and image labels, which effectively addresses the challenge of TCN alignment across images.

CytoCommunity is the first computational tool for end-to-end unsupervised and supervised analyses of single-cell spatial maps and enables direct discovery of conditional-specific cell-cell communication patterns across variable spatial scales.

Please refer to the detailed installation and usage instructions at our GitHub page or


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