Miniscope3D: optimized single-shot miniature 3D fluorescence microscopy

Kyrollos Yanny; Nick Antipa; William Liberti; Sam Dehaeck; Kristina Monakhova; Fanglin Linda Liu; Konlin Shen; Ren Ng; Laura Waller

doi:10.1038/s41377-020-00403-7

Go to Nature Website

Your Location：

Home >

Browse articles >

Miniscope3D: optimized single-shot miniature 3D fluorescence microscopy

Original Articles

- Miniscope3D: optimized single-shot miniature 3D fluorescence microscopy
- Miniscope3D: optimized single-shot miniature 3D fluorescence microscopy
- LSA 2020年9卷第5期页码：1638-1650
- Affiliations：
  
  1.UCB/UCSF Joint Graduate Program in Bioengineering, University of California, Berkeley, CA 94720, USA
  2.Department of Electrical Engineering & Computer Sciences, University of California, Berkeley, CA 94720, USA
  3.TIPs Department, Université libre de Bruxelles (ULB), 1050 Brussels, Belgium
- Author bio：
  
  Kyrollos Yanny (kyrollosyanny@gmail.com)
  Nick Antipa (naantipa@gmail.com)
- Funds：
- DOI：10.1038/s41377-020-00403-7
  中图分类号：
- 纸质出版日期：2020，
  
  网络出版日期：2020-10-02，
  
  收稿日期：2020-05-12，
  
  修回日期：2020-09-01，
  
  录用日期：2020-09-04
- Accepted：
Scan QR Code
Miniscope3D: optimized single-shot miniature 3D fluorescence microscopy[J]. LSA, 2020,9(5):1638-1650.

Yanny, K. et al. Miniscope3D: optimized single-shot miniature 3D fluorescence microscopy. Light: Science & Applications, 9, 1638-1650 (2020).
Miniscope3D: optimized single-shot miniature 3D fluorescence microscopy[J]. LSA, 2020,9(5):1638-1650. DOI： 10.1038/s41377-020-00403-7.

Yanny, K. et al. Miniscope3D: optimized single-shot miniature 3D fluorescence microscopy. Light: Science & Applications, 9, 1638-1650 (2020). DOI： 10.1038/s41377-020-00403-7.

摘要

Abstract

Miniature fluorescence microscopes are a standard tool in systems biology. However

widefield miniature microscopes capture only 2D information

and modifications that enable 3D capabilities increase the size and weight and have poor resolution outside a narrow depth range. Here

we achieve the 3D capability by replacing the tube lens of a conventional 2D Miniscope with an optimized multifocal phase mask at the objective's aperture stop. Placing the phase mask at the aperture stop significantly reduces the size of the device

and varying the focal lengths enables a uniform resolution across a wide depth range. The phase mask encodes the 3D fluorescence intensity into a single 2D measurement

and the 3D volume is recovered by solving a sparsity-constrained inverse problem. We provide methods for designing and fabricating the phase mask and an efficient forward model that accounts for the field-varying aberrations in miniature objectives. We demonstrate a prototype that is 17 mm tall and weighs 2.5 grams

achieving 2.76 μm lateral

and 15 μm axial resolution across most of the 900 × 700 × 390 μm

volume at 40 volumes per second. The performance is validated experimentally on resolution targets

dynamic biological samples

and mouse brain tissue. Compared with existing miniature single-shot volume-capture implementations

our system is smaller and lighter and achieves a more than 2× better lateral and axial resolution throughout a 10× larger usable depth range. Our microscope design provides single-shot 3D imaging for applications where a compact platform matters

such as volumetric neural imaging in freely moving animals and 3D motion studies of dynamic samples in incubators and lab-on-a-chip devices.

关键词

Keywords

references

Ghosh, K. K. et al. Miniaturized integration of a fluorescence microscope.Nat. Methods8, 871–878 (2011)..

Liberti, W. A. Ⅲ et al. J. An open source, wireless capable miniature microscope system.J. Neural Eng.14, 045001 (2017)..

Jacob, A. D. et al. A compact head-mounted endoscope for in vivo calcium imaging in freely behaving mice.Curr. Protoc. Neurosci.84, e51 (2018)..

De Groot, A. et al. NINscope, a versatile miniscope for multi-region circuit investigations.eLife9, e49987 (2020)..

UCLA. Miniscope. athttps://miniscope.orghttps://miniscope.org.

Zong, W. J. et al. Fast high-resolution miniature two-photon microscopy for brain imaging in freely behaving mice.Nat. Methods14, 713–719 (2017)..

Helmchen, F. et al. A miniature head-mounted two-photon microscope: high-resolution brain imaging in freely moving animals.Neuron31, 903–912 (2001)..

Pnevmatikakis, E. A.&Giovannucci, A. NoRMCorre: an online algorithm for piecewise rigid motion correction of calcium imaging data.J. Neurosci. Methods291, 83–94 (2017)..

Engelbrecht, C. J., Voigt, F.&Helmchen, F. Miniaturized selective plane illumination microscopy for high-contrastin vivofluorescence imaging.Opt. Lett.35, 1413–1415 (2010)..

Yanny, K. et al. Miniature 3D fluorescence microscope using random microlenses. Proceedings of Optics and the Brain 2019. Tucson, Arizona United States: Optical Society of America, 2019.

Liu, F. L. et al. Single-shot 3D fluorescence microscopy with Fourier DiffuserCam. Proceedings of Novel Techniques in Microscopy 2019. Tucson, Arizona United States: Optical Society of America, 2019.

Antipa, N. et al. DiffuserCam: lensless single-exposure 3D imaging.Optica5, 1–9 (2018)..

Kuo, G. et al. On-chip fluorescence microscopy with a random microlens diffuser.Opt. Express28, 8384–8399 (2020)..

Adams, J. K. et al. Single-frame 3D fluorescence microscopy with ultraminiature lensless FlatScope.Sci. Adv.3, e1701548 (2017)..

Asif, M. S. et al. FlatCam: replacing lenses with masks and computation. Proceedings of 2015 IEEE International Conference on Computer Vision Workshop (Santiago, Chile: IEEE, 2015).

Levoy, M. etal. Light field microscopy.ACM Trans. Graph.25, 924–934 (2006)..

Broxton, M. et al. Wave optics theory and 3-D deconvolution for the light field microscope.Opt. Express21, 25418–25439 (2013)..

Shin, J. et al. A minimally invasive lens-free computational microendoscope.Sci. Adv.5, eaaw5595 (2019)..

Skocek, O. et al. High-speed volumetric imaging of neuronal activity in freely moving rodents.Nat. Methods15, 429–432 (2018)..

Nöbauer, T. et al. Video rate volumetric Ca2+imaging across cortex using seeded iterative demixing (SID) microscopy.Nat. Methods14, 811–818 (2017)..

Llavador, A. et al. Resolution improvements in integral microscopy with Fourier plane recording.Opt. Express24, 20792–20798 (2016)..

Scrofani, G. et al. FIMic: design for ultimate 3D-integral microscopy of in-vivo biological samples.Biomed. Opt. Express9, 335–346 (2018)..

Guo, C. L. et al. Fourier light-field microscopy.Opt. Express27, 25573–25594 (2019)..

Candès, E. J.&Wakin, M. B. An introduction to compressive sampling.IEEE Signal Proc. Mag.25, 21–30 (2008)..

Candès, E. J.&Fernandez-Granda, C. Towards a mathematical theory of super-resolution.Commun. Pure Appl. Math.67, 906–956 (2014)..

Pavani, S. R. P.&Piestun, R. Three dimensional tracking of fluorescent microparticles using a photon-limited double-helix response system.Opt. Express16, 22048–22057 (2008)..

Beck, A.&Teboulle, M. A fast iterative shrinkage-thresholding algorithm for linear inverse problems.SIAM J. Imag. Sci.2, 183–202 (2009)..

Antipa, N. et al. Video from stills: lensless imaging with rolling shutter. Proceedings of 2019 IEEE International Conference on Computational Photography (Tokyo, Japan: IEEE, 2019).

Katz, O. et al. Non-invasive single-shot imaging through scattering layers and around corners via speckle correlations.Nat. Photonics8, 784–790 (2014)..

Kuo, G. et al. DiffuserCam: diffuser-based lensless cameras. Proceedings of Computational Optical Sensing and Imaging. United States: Optical Society of America (San Francisco, CA, 2017).

Flicker, R. C.&Rigaut, F. J. Anisoplanatic deconvolution of adaptive optics images.J. Opt. Soc. Am. A22, 504–513 (2005)..

Kamilov, U. S. A parallel proximal algorithm for anisotropic total variation minimization.IEEE Trans. Image Process.26, 539–548 (2017)..

Cossairt, O., Gupta, M.&Nayar, S. K. When does computational imaging improve performance?IEEE Trans. Image Process.22, 447–458 (2013)..

Dai, Y. C. et al. Smooth approximation ofL∞-norm for multi-view geometry.2009 Digital Image Computing: Techniques and Applications.(pp. 339–346, Melbourne, VIC, 2009)..

Thiele, S. et al. 3D-printed eagle eye: compound microlens system for foveated imaging.Sci. Adv.3, e1602655 (2017)..

Dehaeck, S., Scheid, B.&Lambert, P. Adaptive stitching for meso-scale printing with two-photon lithography.Addit. Manuf.21, 589–597 (2018)..

Sam Dehaeck. TipSlicer. athttps://github.com/SamDehaeck/TipSlicerhttps://github.com/SamDehaeck/TipSlicer.

浏览量

Downloads

CSCD

文章被引用时，请邮件提醒。

Submit

工具集

关联资源

暂无数据