Researchers at Indian Institute of Technology Kanpur, led by Prof. Hamim Zafar, have developed an advanced computational tool called “Renoir” that enables scientists to decode how cells communicate within complex tissues.

Published in Nature Communications, the study presents a new approach to mapping how signals exchanged between cells influence downstream gene activity in specific spatial environments, addressing a major challenge in biomedical research.

Cells continuously communicate with one another to regulate critical biological processes such as tissue development, immune responses, and disease progression. While recent advances in spatial transcriptomics have enabled researchers to measure gene activity across tissues, understanding how signals from one cell alter the behaviour of another within complex tissue structures has remained difficult.

Renoir addresses this limitation by analysing spatial transcriptomics data — high-resolution maps of gene activity that preserve the exact location of cells within tissues. The tool identifies not only which cells are interacting, but also how these signalling interactions affect downstream genes in distinct tissue regions. This enables researchers to identify “communication niches” where specific signalling pathways are active.

“With Renoir, we can now determine how a specific signalling interaction influences gene activity in the receiving cells,” said Prof. Hamim Zafar. “This opens up new possibilities for identifying disease-driving communication networks and discovering more precise therapeutic targets, especially in complex conditions like cancer.”

“We named our tool Renoir after the French Impressionist artist, as it effectively ‘paints’ the activity of interacting genes across the two-dimensional tissue landscape,” said Narein Rao, a former MS student at IIT Kanpur.

The research was conducted in collaboration with Garvan Institute of Medical Research, Australia, led by Prof. Ankur Sharma. 

The software has been made freely available to the research community through GitHub repository for Renoir.