CUBIC pathology: three-dimensional imaging for pathological diagnosis

Nojima, Satoshi; Susaki, Etsuo A.; Yoshida, Kanji; Takemoto, Hiroyuki; Tsujimura, Naoto; Iijima, Shöhei; Takachi, Ko; Nakahara, Yujiro; Tahara, Shinichiro; Ohshima, Kenji; Kurashige, Masako; Hori, Yumiko; Wada, Naoki; Ikeda, Jun‐ichiro; Kumanogoh, Atsushi; Morii, Eiichi; Ueda, Hiroki R.

doi:10.1038/s41598-017-09117-0

Cited by 122 publications

(154 citation statements)

References 55 publications

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“…Serial sectioning or optical‐ablative methods, in combination with 3D image reconstruction, are labor‐ and computation‐intensive, requiring acquisition times of days to obtain single‐cell resolution,5 and still hinder continuous observations 6. Technically demanding protocols for rendering tissue optically transparent, for example, CLARITY,5, 7 PACT,8 or CUBIC,6 remain time‐consuming and, subsequently to tissue clearing, powerful histology can only partially be applied, due to stain or antibody binding reduction or tissue degradation.…”

Section: Introductionmentioning

confidence: 99%

Hard X‐Ray Nanoholotomography: Large‐Scale, Label‐Free, 3D Neuroimaging beyond Optical Limit

et al. 2018

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There have been great efforts on the nanoscale 3D probing of brain tissues to image subcellular morphologies. However, limitations in terms of tissue coverage, anisotropic resolution, stain dependence, and complex sample preparation all hinder achieving a better understanding of the human brain functioning in the subcellular context. Herein, X‐ray nanoholotomography is introduced as an emerging synchrotron radiation‐based technology for large‐scale, label‐free, direct imaging with isotropic voxel sizes down to 25 nm, exhibiting a spatial resolution down to 88 nm. The procedure is nondestructive as it does not require physical slicing. Hence, it allows subsequent imaging by complementary techniques, including histology. The feasibility of this 3D imaging approach is demonstrated on human cerebellum and neocortex specimens derived from paraffin‐embedded tissue blocks. The obtained results are compared to hematoxylin and eosin stained histological sections and showcase the ability for rapid hierarchical neuroimaging and automatic rebuilding of the neuronal architecture at the level of a single cell nucleolus. The findings indicate that nanoholotomography can complement microscopy not only by large isotropic volumetric data but also by morphological details on the sub‐100 nm level, addressing many of the present challenges in brain tissue characterization and probably becoming an important tool in nanoanatomy.

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Section: Introductionmentioning

confidence: 99%

Hard X‐Ray Nanoholotomography: Large‐Scale, Label‐Free, 3D Neuroimaging beyond Optical Limit

et al. 2018

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“…One major impediment is that tissues can undergo multiple rounds of expansion and/or shrinkage during the clearing process. However, change in size does not result in tissue disruption in the final cleared product and has minimal impact on outcomes 3,14,17 . In fact, increasing tissue volume can be used to increase resolution 18,19 , whereas decreasing the volume can be advantageous for large samples [20][21][22] .…”

Section: Introductionmentioning

confidence: 99%

“…The ability to synthesise hydrogels with tuneable physical and chemical characteristics makes them a favourable material for use in tissue engineering, ophthalmology, wound-dressing and various other biomedical applications29 . Herein, we evaluated the applicability of a high refractive index hydrogel that provided stability to tissue architecture and minimised shrinking/expanding of the tissue for use in imaging large biological samples with LSFM6,17 . Typically, hydrogels have either a high refractive index or high-water content, but not both.…”

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confidence: 99%

Use of high-refractive index hydrogels and tissue clearing for large biological sample imaging

Richardson

Fok²,

Lee

et al. 2020

Preprint

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Recent advances in tissue clearing and light sheet fluorescence microscopy have improved insights into and understanding of tissue morphology and disease pathology by imaging large samples without the requirement of histological sectioning. However, sample handling and conservation of sample integrity during lengthy staining and acquisition protocols remains a challenge. This study overcomes these challenges with acrylamide hydrogels synthesised to match the refractive index of solutions typically utilised in aqueous tissue clearing protocols.These hydrogels have a high-water content (82.0±3.7% by weight). The gels are stable over time and FITC-IgG readily permeated into, and effluxed out of them. Whilst the gels deformed and/or swelled over time in some commonly used solutions, this was overcome by using a previously described custom RIMS solution. To validate their use, CUBIC cleared mouse tissues and whole embryos were embedded in hydrogels, stained using fluorescent small molecule dyes, labels and antibodies and successfully imaged using light sheet fluorescence microscopy. In conclusion, the high-water content, high refractive index hydrogels described in this study have a broad applicability to research that delves into pathophysiological processes by stabilisating and protecting large and fragile samples.

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“…While a macroscopic anatomical picture of 17 the brain is easily acquired non invasively or ex vivo with magnetic resonance imaging (MRI), 18 finer characterization requires histological procedures and microscopy. Histology and MRI are 19 highly complementary modalities: histology produces excellent contrast at the microscopic scale 20 using dedicated stains that target different microanatomical or cytoarchitectural features, but it 21 is a 2D modality that also inevitably introduces distortions in the tissue during blocking and 22 sectioning. MRI does not yield microscopic resolution, but produces undistorted 3D volumes.…”

mentioning

confidence: 99%

“…Notably, large-scale microtomes are not a feasible solution with these techniques, 59 as they are inherently limited to small tissue blocks. In fact, despite technological advances 60 in terms of both increasingly larger samples [17][18][19] and novel microscopic acquisitions [20,21], 61 complete multi-scale characterization of the human brain as a whole organ still requires the use 62 of complementary tools able to cover all the biologically relevant scales. This inherent limitation 63 makes the development of inter-modality workflows a necessity, especially as cutting-edge research 64 starts to target the whole human body [22].…”

mentioning

confidence: 99%

A multimodal computational pipeline for 3D histology of the human brain

Mancini

Casamitjana

Peter

et al. 2020

Preprint

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Ex vivo imaging enables analysis of the human brain at a level of detail that is not possible in vivo with MRI. In particular, histology can be used to study brain tissue at the microscopic level, using a wide array of different stains that highlight different microanatomical features. Complementing MRI with histology has important applications in ex vivo atlas building and in modeling the link between microstructure and macroscopic MR signal. However, histology requires sectioning tissue, hence distorting its 3D structure, particularly in larger human samples. Here, we present an open-source computational pipeline to produce 3D consistent histology reconstructions of the human brain. The pipeline relies on a volumetric MRI scan that serves as undistorted reference, and on an intermediate imaging modality (blockface photography) that bridges the gap between MRI and histology. We present results on 3D histology reconstruction of a whole human hemisphere.1/26 33 1. Cutting and sectioning of tissue for histology introduces distortions (stretching, tearing, 34 folding, cracking, see [6]) that are specific to each section. Therefore, an external volumetric 35 reference (typically an MRI scan) is required to produce an unbiased registration. Without 36 such a reference, naïve pairwise registration leads to accumulation of errors ("z-shift") and 37 spurious straightening of curved structures (the so-called "banana effect", [7]). 382. Large differences in contrast and resolution between MRI and histology, combined with 39 potential inhomogeneous staining and the aforementioned sectioning artifacts, make the 40 alignment of these two modalities a difficult inter-modality registration problem. 413. The large size of the human brain, compared with most animal models, requires cutting 42 the tissue in blocks for whole-brain analyses, with the resulting need to reassemble the 43 blocks [6], which is a part-to-whole registration problem [8,9]. This problem can be solved 44 with whole brain microtomes, although such microtomes are only available in few selected 45 sites around the world. Moreover, they exacerbate the sectioning artifacts, due to the much 46 larger surface area of the sections. 47Even when a reference MRI is available, 3D histology reconstruction is an ill-posed problem, 48 as errors in the -typically linear -registration between the MRI and the histological stack 49 2/26

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CUBIC pathology: three-dimensional imaging for pathological diagnosis

Cited by 122 publications

References 55 publications

Hard X‐Ray Nanoholotomography: Large‐Scale, Label‐Free, 3D Neuroimaging beyond Optical Limit

Hard X‐Ray Nanoholotomography: Large‐Scale, Label‐Free, 3D Neuroimaging beyond Optical Limit

Use of high-refractive index hydrogels and tissue clearing for large biological sample imaging

A multimodal computational pipeline for 3D histology of the human brain

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