Nasir-Moin, M. et al. Localization of protoporphyrin IX during glioma-resection surgery via paired stimulated Raman histology and fluorescence microscopy. Nat. Biomed. Eng. 8, 672–688 (2024).
Article CAS PubMed Google Scholar
Kanatani, S. et al. Whole-brain spatial transcriptional analysis at cellular resolution. Science 386, 907–915 (2024).
Article CAS PubMed Google Scholar
Sylwestrak, E. L., Rajasethupathy, P., Wright, M. A., Jaffe, A. & Deisseroth, K. Multiplexed intact-tissue transcriptional analysis at cellular resolution. Cell 164, 792–804 (2016).
Article CAS PubMed PubMed Central Google Scholar
Ji, N. Adaptive optical fluorescence microscopy. Nat. Methods 14, 374–380 (2017).
Article CAS PubMed Google Scholar
Peng, B. et al. Practical guidelines for cell segmentation models under optical aberrations in microscopy. Comput. Struct. Biotechnol. J. 26, 23–39 (2024).
Article PubMed PubMed Central Google Scholar
Chen, W. et al. In vivo volumetric imaging of calcium and glutamate activity at synapses with high spatiotemporal resolution. Nat. Commun. 12, 6630 (2021).
Article CAS PubMed PubMed Central Google Scholar
Hampson, K. M. et al. Adaptive optics for high-resolution imaging. Nat. Rev. Methods Prim. 1, 1–26 (2021).
Velasco, M. G. M. et al. 3D super-resolution deep-tissue imaging in living mice. Optica 8, 442–450 (2021).
Article PubMed PubMed Central Google Scholar
Wang, K. et al. Rapid adaptive optical recovery of optimal resolution over large volumes. Nat. Methods 11, 625–628 (2014).
Article CAS PubMed PubMed Central Google Scholar
Schubert, M. C. et al. Deep intravital brain tumor imaging enabled by tailored three-photon microscopy and analysis. Nat. Commun. 15, 7383 (2024).
Article CAS PubMed PubMed Central Google Scholar
Streich, L. et al. High-resolution structural and functional deep brain imaging using adaptive optics three-photon microscopy. Nat. Methods 18, 1253–1258 (2021).
Article CAS PubMed PubMed Central Google Scholar
Kang, I., Zhang, Q., Yu, S. X. & Ji, N. Coordinate-based neural representations for computational adaptive optics in widefield microscopy. Nat. Mach. Intell. 6, 714–725 (2024).
Hu, Q. et al. Universal adaptive optics for microscopy through embedded neural network control. Light Sci. Appl. 12, 270 (2023).
Article CAS PubMed PubMed Central Google Scholar
Zhang, Y. et al. Conformal convolutional neural network (CCNN) for single-shot sensorless wavefront sensing. Opt. Express 28, 19218 (2020).
Guo, M. et al. Deep learning-based aberration compensation improves contrast and resolution in fluorescence microscopy. Nat. Commun. 16, 313 (2025).
Article CAS PubMed PubMed Central Google Scholar
Wu, J. et al. Iterative tomography with digital adaptive optics permits hour-long intravital observation of 3D subcellular dynamics at millisecond scale. Cell 184, 3318–3332 (2021).
Article CAS PubMed Google Scholar
Jogin, M. et al. Feature extraction using convolution neural networks (CNN) and deep learning. In Proc. 3rd International Conference on Recent Trends in Electronics, Information & Communication Technology https://doi.org/10.1109/RTEICT42901.2018.9012507 (IEEE, 2018).
Liang, H., Sun, X., Sun, Y. & Gao, Y. Text feature extraction based on deep learning: a review. EURASIP J. Wirel. Commun. Netw. 2017, 211 (2017).
Article PubMed PubMed Central Google Scholar
Shaheen, F., Verma, B. & Asafuddoula, M. D. Impact of automatic feature extraction in deep learning architecture. In Proc. International Conference on Digital Image Computing: Techniques and Applications https://doi.org/10.1109/DICTA.2016.7797053 (IEEE, 2016).
Chen, B. et al. Automated discovery of fundamental variables hidden in experimental data. Nat. Comput. Sci. 2, 433–442 (2022).
Higgins, I. et al. Unsupervised deep learning identifies semantic disentanglement in single inferotemporal face patch neurons. Nat. Commun. 12, 6456 (2021).
Article CAS PubMed PubMed Central Google Scholar
Zhang, C. et al. A large, switchable optical clearing skull window for cerebrovascular imaging. Theranostics 8, 2696–2708 (2018).
Article CAS PubMed PubMed Central Google Scholar
Silasi, G., Xiao, D., Vanni, M. P., Chen, A. C. N. & Murphy, T. H. Intact skull chronic windows for mesoscopic wide-field imaging in awake mice. J. Neurosci. Methods 267, 141–149 (2016).
Article PubMed PubMed Central Google Scholar
de Haan, K., Rivenson, Y., Wu, Y. & Ozcan, A. Deep-learning-based image reconstruction and enhancement in optical microscopy. Proc. IEEE 108, 30–50 (2020).
Reichstein, M. et al. Deep learning and process understanding for data-driven Earth system science. Nature 566, 195–204 (2019).
Article CAS PubMed Google Scholar
Mathieu, E., Rainforth, T., Siddharth, N. & Teh, Y. W. Disentangling disentanglement in variational autoencoders. In Proc. 36th International Conference on Machine Learning (eds Chaudhuri, K. & Sugiyama, M.) 4402–4412 (PMLR, 2019).
Brahma, P. P., Wu, D. & She, Y. Why deep learning works: a manifold disentanglement perspective. IEEE Trans. Neural Netw. Learn. Syst. 27, 1997–2008 (2016).
Zheng, Z. & Sun, L. Disentangling latent space for VAE by label relevant/irrelevant dimensions. In Proc. IEEE/CVF Conference on Computer Vision and Pattern Recognition 12192–12201 (2019).
Lu, Z. et al. Phase-space deconvolution for light field microscopy. Opt. Express 27, 18131–18145 (2019).
Liu, D. et al. T–B-cell entanglement and ICOSL-driven feed-forward regulation of germinal centre reaction. Nature 517, 214–218 (2015).
Article CAS PubMed Google Scholar
Mao, T. et al. Long-range neuronal circuits underlying the interaction between sensory and motor cortex. Neuron 72, 111–123 (2011).
Article CAS PubMed PubMed Central Google Scholar
Meiniel, W., Olivo-Marin, J.-C. & Angelini, E. D. Denoising of microscopy images: a review of the state-of-the-art, and a new sparsity-based method. IEEE Trans. Image Process. 27, 3842–3856 (2018).
Mandracchia, B. et al. Fast and accurate sCMOS noise correction for fluorescence microscopy. Nat. Commun. 11, 94 (2020).
Article CAS PubMed PubMed Central Google Scholar
Liang, C.-K., Lin, T.-H., Wong, B.-Y., Liu, C. & Chen, H. H. Programmable aperture photography: multiplexed light field acquisition. In ACM SIGGRAPH 2008 papers https://doi.org/10.1145/1399504.1360654 (ACM, 2008).
Prevedel, R. et al. Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy. Nat. Methods 11, 727–730 (2014).
Article CAS PubMed PubMed Central Google Scholar
Lu, Z. et al. Long-term intravital subcellular imaging with confocal scanning light-field microscopy. Nat. Biotechnol. 43, 569–580 (2025).
Comments (0)