Introduction 1 5 6 3 7 8 omic 1 9 11 Fig. 1 left right  Advances in fluorescent probes Aequorea Labeling of biomolecules with fluorescent probes or other dyes has facilitated in vitro or in vivo studies of biomolecular structures and dynamics, as well as their interactions, which is critical if we are to understand the biomolecular mechanisms of cellular function. However, traditional methods of chemical labeling based on fluorescent dyes are often inadequate for biomolecular labeling, repurification and reintroduction into cells by invasive methods like microinjection. These limitations have spawned efforts to noninvasively and site-specifically label protein in living cells or tissues by using green fluorescent protein (GFP) and its variants. The fluorescent protein presents a relatively small size and a compact, single-domain structure, which allow it to fuse to other targeted proteins with little or no interference in native protein. Aequorea victoria 2 12 13 14 15 16 17 18 Fig. 2a–c a b c  Other kinds of fluorescent protein Discosoma genus 19 20 21 2 22 23 24 Fungia concinn 25 26 Trachyphyllia geoffroyi New rearrangement variants of fluorescent protein 2 K a 27 28 Nongenetic fluorescent probes C. elegans Drosophila 29 30 31 32 33 34 3 35 36 Fig. 3 Method of conjugating QDs to target proteins. The pG-zb acts as a molecular adaptor, connecting the QDs with the target protein through interactions of its protein G portion with a specific antibody as well as interactions of its positively charged tail with QDs capped with a negatively charged dihydrolipoic acid surface  OMI techniques General imaging microscopy 4 37 38 37 38 Fig. 4a–f a b c d 51 e red yellow 57 f black 59  39 4 40 Second-harmonic imaging microscopy (SHIM) 41 Optical coherence tomography (OCT) 42 43 44 Fluorescent molecular imaging approaches Fluorescence resonance energy transfer (FRET) 4 45 46 47 46 48 47 49 Fluorescence recovery after photobleaching (FRAP) 4 50 51 52 Fluorescence lifetime imaging microscopy (FLIM) 53 54 4 55 56 57 Fluorescence correlation spectroscopy (FCS) 4 58 59 60 Applications of OMI OMI for biomolecules 61 62 63 64 65 66 67 68 46 69 2+ 70 Using OMI to monitor physiological processes in living cells Monitoring gene expression and RNA localization 71 72 73 74 75 76 Monitoring protein and subcellular organelle dynamics 77 78 79 80 Arabidopsis 81 82 Monitoring general protein–protein interactions 5 83 84 85 46 86 6 87 88 Fig. 5a–d a b c d  Fig. 6a–d a b c d − +  Monitoring protease and kinase activity 89 5 90 92 93 5 94 95 96 Monitoring changes in calcium 97 2+ 5 28 98 99 2+ 2+ 2+ 100 6 14 27 6 101 Monitoring changes in cyclic nucleotides 102 103 5 104 105 106 105 Monitoring changes in transmembrane voltage 107 + + + 108 109 Monitoring changes in pH in living cells 12 6 Renilla reniformis 110 111 112 Monitoring signal transduction from cell to cell 113 114 115 Using OMI to investigate tissue structure and function 116 C. elegans 117 118 119 120 121 122 123 124 125 126 127 128 OMI of organisms Employing fluorescent protein 129 C. elegans 130 C. elegans 2+ 7 131 132 133 C. elegans 2+ Drosophila 134 7 135 7 136 137 138 139 140 Fig. 7a–k 2+ a b red color C. elegans 130 c f 2+ Drosophila 135 g h i 136 j k 33  Employing QDs 141 33 7 142 1 Table 1 OMI in systems biology Techniques Physical processes Resolution Sensitivity Penetration Observation methods Probes Indicator localization References WFM LSCM MPLSM RNA transcription and expression High High High DFI, FRET FPs In vitro, cells, tissues, organism 63 64 71 76 Protein localization and dynamics    DFI FPs In vitro, cells, tissues, organism 51 52 65 77 79 Subcellular organelle dynamics    DFI, FRAP FPs Cells 80 82 Protein interaction    FRET, FLIM, FCS FPs, cpFPs Cells, mouse 46 47 49 57 59 60 83 88 140 Protease and kinase activity    FRET FPs  89 96 Calcium    DFI, FRET FPs, cpFPs C. elegans Drosophila 14 27 28 97 101 130 138 cAMP, cGMP    FRET FPs Cells 102 106 Electrical activity    DFI, FRET FPs Cells 107 109 pH    DFI, FRET FPs Cells, mouse 110 112 139 Tumor    DFI QDs Mouse 33 141 142 SHIM Biomacromolecules Low High Low NI – C. elegans 116 118 Membrane potential    NI Dyes Cells, brain tissue 119 120 OCT Morphology of tissue High Low High EI – Human 122 123 Activity and disease of organ    EI – Human 124 125 RS Composition of structure Low High Low NI – Brain tissues, bronchial tissue 126 127 FT-IR Kinetics of reaction intermediates Low High Low NI – Yeast extract, fish liver 67 68 DFI NI EI Future development 8 143 144 145