Note: Eliminating stripe artifacts in light-sheet fluorescence imaging

Salili, Seyyed Muhammad; Harrington, Matt; Durian, Douglas J.

doi:10.1063/1.5016546

Cited by 14 publications

(12 citation statements)

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“…The pivoting is realized by means of a single Acousto-Optic Deflector, which can generate either multiple static or a single dynamically swept light-sheet. Such method allows to obtain images readily useable for subsequent analysis, without requiring computationally and time costly post-processing like in a multi-view acquisition approach (Krzic et al, 2012) or in algorithmic pixel intensity variation compensation (Liang et al, 2016; Salili et al, 2018). The cost and difficulty of implementing an AOD solution is much lower than using non-Gaussian beams (Fahrbach et al, 2010; Vettenburg et al, 2014; Müllenbroich et al, 2018) and is comparable with a galvanometric mirror based approach (Huisken and Stainier, 2007), with the advantage of increased flexibility and pivoting rate (up to several MHz, depending on the AOD specifications, in particular its acoustic wave propagation velocity and the input beam size), effectively removing any limit on the imaging framerate when using a static 7LS configuration.…”

Section: Discussionmentioning

confidence: 99%

“…Such method is time consuming and hardly feasible when imaging of fast biological processes is required, such as neuron activity (Ahrens et al, 2013) and blood cell flow (Fahrbach et al, 2013). Image post-processing has been reported as a method, but it can potentially introduce new artifacts since most algorithms are based on pixel intensity variation compensation which is not robust at low SBR (Liang et al, 2016; Salili et al, 2018). Moreover non-Gaussian beams (Fahrbach et al, 2010; Vettenburg et al, 2014) can be used to reduce striping artifacts.…”

Section: Introductionmentioning

confidence: 99%

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Flexible Multi-Beam Light-Sheet Fluorescence Microscope for Live Imaging Without Striping Artifacts

et al. 2019

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The development of light-sheet fluorescence microscopy (LSFM) has greatly expanded the experimental capabilities in many biological and biomedical research fields, enabling for example live studies of murine and zebrafish neural activity or of cell growth and division. The key feature of the method is the selective illumination of a sample single plane, providing an intrinsic optical sectioning and allowing direct 2D image recording. On the other hand, this excitation scheme is more affected by absorption or scattering artifacts in comparison to point scanning methods, leading to un-even illumination. We present here an easily implementable method, based on acousto-optical deflectors (AOD), to overcome this obstacle. We report the advantages provided by flexible and fast AODs in generating simultaneous angled multiple beams from a single laser beam and in fast light sheet pivoting and we demonstrate the suppression of illumination artifacts.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Flexible Multi-Beam Light-Sheet Fluorescence Microscope for Live Imaging Without Striping Artifacts

et al. 2019

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“…Another artifact that can bias analyses is the striping artifact common to most LSFM implementations. Resonant scanning of the light sheet prevents the artifact 54 , but newer approaches using static optics 55,56 are more compatible with the miniature illumination path of OCPI and will be integrated in future work.…”

Section: Discussionmentioning

confidence: 99%

Fast objective coupled planar illumination microscopy

Greer

Holy

2019

Nat Commun

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Among optical imaging techniques light sheet fluorescence microscopy is one of the most attractive for capturing high-speed biological dynamics unfolding in three dimensions. The technique is potentially millions of times faster than point-scanning techniques such as two-photon microscopy. However light sheet microscopes are limited by volume scanning rate and/or camera speed. We present speed-optimized Objective Coupled Planar Illumination (OCPI) microscopy, a fast light sheet technique that avoids compromising image quality or photon efficiency. Our fast scan system supports 40 Hz imaging of 700 μm-thick volumes if camera speed is sufficient. We also address the camera speed limitation by introducing Distributed Planar Imaging (DPI), a scaleable technique that parallelizes image acquisition across cameras. Finally, we demonstrate fast calcium imaging of the larval zebrafish brain and find a heartbeat-induced artifact, removable when the imaging rate exceeds 15 Hz. These advances extend the reach of fluorescence microscopy for monitoring fast processes in large volumes.

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“…Stripe artifacts are commonplace in images acquired with LSFM due to irregularities in the refractive index (RI) of the sample 3,11 . This RI mismatch can be compensated for using an immersion medium that has a similar RI to that of the sample 12 .…”

Section: Development Of the Destriping Modulementioning

confidence: 99%

“…Current strategies for image destriping are either based on optical filtering or digital filtering 11,[13][14][15] . Optical filtering strategies attempt to compensate for RI mismatch during imaging, effectively removing the stripe artifacts from the source.…”

Section: Development Of the Destriping Modulementioning

confidence: 99%

Scalable image processing techniques for quantitative analysis of volumetric biological images from light-sheet microscopy

Swaney

Kamentsky

Evans

et al. 2019

Preprint

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Here we describe an image processing pipeline for quantitative analysis of terabyte-scale volumetric images of SHIELD-processed mouse brains imaged with light-sheet microscopy. The pipeline utilizes open-source packages for destriping, stitching, and atlas alignment that are optimized for parallel processing. The destriping step removes stripe artifacts, corrects uneven illumination, and offers over 100x speed improvements compared to previously reported algorithms. The stitching module builds upon Terastitcher to create a single volumetric image quickly from individual image stacks with parallel processing enabled by default. The atlas alignment module provides an interactive web-based interface that automatically calculates an initial alignment to a reference image which can be manually refined. The atlas alignment module also provides summary statistics of fluorescence for each brain region as well as region segmentations for visualization. The expected runtime of our pipeline on a whole mouse brain hemisphere is 1-2 d depending on the available computational resources and the dataset size.Recently, LSFM images of a whole mouse brain have been used to create a single-cell mouse brain atlas 4 . The pipeline consisted of a heterogeneous mix of MATLAB, Python, and C++ software as well as expensive computer hardware, including a dedicated image processing server equipped with four NVIDIA graphics processing units (GPU). In order to handle individual volumetric images that are larger than the amount of available memory, images were processed slice-by-slice for cell detection and rescaled to a manageable size for atlas alignment. Although computationally impressive, such tools often require a great deal of programming expertise or access to proprietary software. As a result, the current large-scale image processing pipelines may be inaccessible to non-experts, and there is a need for large-scale image processing tools for researchers focused on biological questions rather than computational challenges.The protocols presented here are designed to be easy to setup and applicable to users without much experience in setting up complex development environments. Since some users may only want to use part of our pipeline, the protocols are partitioned into three computational modules: first, our image destriping for removing streaks and performing flat-field correction in raw LSFM images; second, stitching for creating a single 3D image from the individual 2D images; and third,

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Note: Eliminating stripe artifacts in light-sheet fluorescence imaging

Cited by 14 publications

References 49 publications

Flexible Multi-Beam Light-Sheet Fluorescence Microscope for Live Imaging Without Striping Artifacts

Flexible Multi-Beam Light-Sheet Fluorescence Microscope for Live Imaging Without Striping Artifacts

Fast objective coupled planar illumination microscopy

Scalable image processing techniques for quantitative analysis of volumetric biological images from light-sheet microscopy

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