biostudies-literatureLi SNational Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint FundNational Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)The Innovation Fund of the Wuhan National Laboratory for Optoelectronics.3808https://www.ebi.ac.uk/biostudies/studies/S-EPMC12019549biostudies-literatureUnknown16(1)Raman spectroscopy, which probes fine molecular vibrations, is crucial for interpreting covalent bonds, chemical compositions, and other molecular dynamics in mixtures via their vibrational fingerprint signatures. However, over the past few decades, longstanding barriers have been encountered in both the sensitivity and speed of Raman spectroscopy, limiting its ability to be extended to broader biochemical applications. Here, we introduce a versatile analytical workhorse, the fiber-array Raman engine (termed FIRE). In FIRE, a distinctive fiber array bundle delays the Raman shifts at a scale of 3-960 ns, and a highly dynamic single-channel photon-counting detector achieves spectral measurements that outperform the best commercial confocal Raman microscope. Crucially, FIRE features a major aNature communicationsPhoton-counting Raman spectroscopy at a MHz spectral rate for biochemical imaging of an entire organism.PMC120195496142106461675075Li HLiu JZhou QLu WLv XYan SZhang QLiu XLi YWang PLi SXiao LShen AHuang ZWang SChen YZhang BWang ZfalsePhoton-counting Raman spectroscopy at a MHz spectral rate for biochemical imaging of an entire organism.Raman spectroscopy, which probes fine molecular vibrations, is crucial for interpreting covalent bonds, chemical compositions, and other molecular dynamics in mixtures via their vibrational fingerprint signatures. However, over the past few decades, longstanding barriers have been encountered in both the sensitivity and speed of Raman spectroscopy, limiting its ability to be extended to broader biochemical applications. Here, we introduce a versatile analytical workhorse, the fiber-array Raman engine (termed FIRE). In FIRE, a distinctive fiber array bundle delays the Raman shifts at a scale of 3-960 ns, and a highly dynamic single-channel photon-counting detector achieves spectral measurements that outperform the best commercial confocal Raman microscope. Crucially, FIRE features a major a2025-01-01T00:00:00Z2025 Apr2025-07-06T03:04:13.956Z2025-07-06T03:04:13.956ZS-EPMC120195494026891210.1038/s41467-025-59030-8