Rice is a global staple crop that has a large requirement of water at various growth and developmental stages. As a matter of fact, drought can substantially reduce rice yield. The traits responsible for drought tolerance can be selected and studied to improve rice growth and yield under stress conditions. In the present study, morphological, physiological, biochemical and molecular variations between drought tolerant (PB6 and Moroberakan) and drought sensitive (Way Rarem) varieties have been evaluated. Notable differences have been observed in root morphology, root xylem number and area, stomata number, relative water content, proline content, protein and gene expression. In addition, novel automated frameworks based on computer vision algorithms have been employed for high-throughput quantification of xylem using scanning electron microscopy images. Transcriptome analysis has revealed variation in expression of Med37c and RSOsPR10 genes among various rice varieties. The differential proteome analysis using 2-D followed by MALDI-based identification implied the role of chitinases in drought tolerance. The information generated from computational/digital image analysis as well as biochemical studies can contribute significantly towards the developing field of rice phenomics. © 2019 Elsevier B.V.