Fast confocal Raman imaging via context-aware compressive sensing

Raman hyperspectral imaging is a powerful method to obtain detailed chemical information about a wide variety of organic and inorganic samples noninvasively and without labels. However, due to the weak, nonresonant nature of spontaneous Raman scattering, acquiring a Raman imaging dataset is time-consuming and inefficient. In this paper we utilize a compressive imaging strategy coupled with a context-aware image prior to improve Raman imaging speed by 5- to 10-fold compared to classic point-scanning Raman imaging, while maintaining the traditional benefits of point scanning imaging, such as isotropic resolution and confocality. With faster data acquisition, large datasets can be acquired in reasonable timescales, leading to more reliable downstream analysis. On standard samples, context-aware Raman compressive imaging (CARCI) was able to reduce the number of measurements by ∼85% while maintaining high image quality (SSIM >0.85). Using CARCI, we obtained a large dataset of chemical images of fission yeast cells, showing that by collecting 5-fold more cells in a given experiment time, we were able to get more accurate chemical images, identification of rare cells, and improved biochemical modeling. For example, applying VCA to nearly 100 cells' data together, cellular organelles were resolved that were not faithfully reconstructed by a single cell's dataset.