image: ImSpiRE enhances spatial resolution in three steps: it first extracts image features from spots and patches based on histological images, then computes the relationships between spots and patches, and finally redistributes gene expression data across patches using an optimal transport method. This process produces enhanced transcriptional profiles with higher resolution.
Credit: ©Science China Press
Current spatially resolved transcriptomic technologies often struggle to achieve the necessary resolution to analyze individual cells within tissues, which limits their utility in uncovering fine-scale biological details. ImSpiRE, developed by Prof. Yong Zhang and his team at Tongji University, offers a breakthrough solution. By using histological image features to enhance the spatial resolution of gene expression data, ImSpiRE is able to redistribute transcriptional profiles across tissue sections. This method overcomes the limitations of existing techniques, allowing for a finer resolution that captures subspot-level detail.
ImSpiRE works by addressing an optimal transport problem, redistributing gene expression data from larger transcriptomic spots to smaller patches. These patches are more representative of actual tissue structures, enabling researchers to visualize gene expression with unprecedented clarity. Importantly, ImSpiRE does not require additional single-cell data or prior knowledge, making it widely applicable across different spatial transcriptomic datasets. It can even reconstruct expression profiles in unmeasured regions, something previous methods were unable to achieve.
The team has applied ImSpiRE on various datasets, including mouse tissue and human tumor samples. The enhanced resolution provided by ImSpiRE not only reveals intricate tissue structures but also aids in identifying tissue domains and detecting complex interactions, such as ligand-receptor signaling pathways within tumors. These capabilities open new avenues for understanding disease progression and tissue development.
By providing a clearer view of how genes are expressed in tissues, ImSpiRE opens up new possibilities for researchers, helping them dive deeper into the complex workings of cells and tissues. This advancement will benefit fields like cancer research, neuroscience, and developmental biology.
Journal
Science China Life Sciences