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Tajbakhsh K, Stanowska O, Neels A, Perren A, Zboray R. 3D Virtual Histopathology by Phase-Contrast X-Ray Micro-CT for Follicular Thyroid Neoplasms. IEEE TRANSACTIONS ON MEDICAL IMAGING 2024; 43:2670-2678. [PMID: 38437150 DOI: 10.1109/tmi.2024.3372602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
Histological analysis is the core of follicular thyroid carcinoma (FTC) classification. The histopathological criteria of capsular and vascular invasion define malignancy and aggressiveness of FTC. Analysis of multiple sections is cumbersome and as only a minute tissue fraction is analyzed during histopathology, under-sampling remains a problem. Application of an efficient tool for complete tissue imaging in 3D would speed-up diagnosis and increase accuracy. We show that X-ray propagation-based imaging (XPBI) of paraffin-embedded tissue blocks is a valuable complementary method for follicular thyroid carcinoma diagnosis and assessment. It enables a fast, non-destructive and accurate 3D virtual histology of the FTC resection specimen. We demonstrate that XPBI virtual slices can reliably evaluate capsular invasions. Then we discuss the accessible morphological information from XPBI and their significance for vascular invasion diagnosis. We show 3D morphological information that allow to discern vascular invasions. The results are validated by comparing XPBI images with clinically accepted histology slides revised by and under supervision of two experienced endocrine pathologists.
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Duan X, Ding XF, Li N, Wu FX, Chen X, Zhu N. Sparse2Noise: Low-dose synchrotron X-ray tomography without high-quality reference data. Comput Biol Med 2023; 165:107473. [PMID: 37690288 DOI: 10.1016/j.compbiomed.2023.107473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/12/2023]
Abstract
BACKGROUND Synchrotron radiation computed tomography (SR-CT) holds promise for high-resolution in vivo imaging. Notably, the reconstruction of SR-CT images necessitates a large set of data to be captured with sufficient photons from multiple angles, resulting in high radiation dose received by the object. Reducing the number of projections and/or photon flux is a straightforward means to lessen the radiation dose, however, compromises data completeness, thus introducing noises and artifacts. Deep learning (DL)-based supervised methods effectively denoise and remove artifacts, but they heavily depend on high-quality paired data acquired at high doses. Although algorithms exist for training without high-quality references, they struggle to effectively eliminate persistent artifacts present in real-world data. METHODS This work presents a novel low-dose imaging strategy namely Sparse2Noise, which combines the reconstruction data from paired sparse-view CT scan (normal-flux) and full-view CT scan (low-flux) using a convolutional neural network (CNN). Sparse2Noise does not require high-quality reconstructed data as references and allows for fresh training on data with very small size. Sparse2Noise was evaluated by both simulated and experimental data. RESULTS Sparse2Noise effectively reduces noise and ring artifacts while maintaining high image quality, outperforming state-of-the-art image denoising methods at same dose levels. Furthermore, Sparse2Noise produces impressive high image quality for ex vivo rat hindlimb imaging with the acceptable low radiation dose (i.e., 0.5 Gy with the isotropic voxel size of 26 μm). CONCLUSIONS This work represents a significant advance towards in vivo SR-CT imaging. It is noteworthy that Sparse2Noise can also be used for denoising in conventional CT and/or phase-contrast CT.
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Affiliation(s)
- Xiaoman Duan
- Division of Biomedical Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada
| | - Xiao Fan Ding
- Division of Biomedical Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada
| | - Naitao Li
- Division of Biomedical Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada
| | - Fang-Xiang Wu
- Division of Biomedical Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada; Department of Computer Science, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada; Department of Mechanical Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada
| | - Xiongbiao Chen
- Division of Biomedical Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada; Department of Mechanical Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada.
| | - Ning Zhu
- Division of Biomedical Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada; Canadian Light Source, Saskatoon, S7N 2V3, SK, Canada; Department of Chemical and Biological Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada.
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Rodgers G, Bikis C, Janz P, Tanner C, Schulz G, Thalmann P, Haas CA, Müller B. 3D X-ray Histology for the Investigation of Temporal Lobe Epilepsy in a Mouse Model. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1730-1745. [PMID: 37584515 DOI: 10.1093/micmic/ozad082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/29/2023] [Accepted: 07/28/2023] [Indexed: 08/17/2023]
Abstract
The most common form of epilepsy among adults is mesial temporal lobe epilepsy (mTLE), with seizures often originating in the hippocampus due to abnormal electrical activity. The gold standard for the histopathological analysis of mTLE is histology, which is a two-dimensional technique. To fill this gap, we propose complementary three-dimensional (3D) X-ray histology. Herein, we used synchrotron radiation-based phase-contrast microtomography with 1.6 μm-wide voxels for the post mortem visualization of tissue microstructure in an intrahippocampal-kainate mouse model for mTLE. We demonstrated that the 3D X-ray histology of unstained, unsectioned, paraffin-embedded brain hemispheres can identify hippocampal sclerosis through the loss of pyramidal neurons in the first and third regions of the Cornu ammonis as well as granule cell dispersion within the dentate gyrus. Morphology and density changes during epileptogenesis were quantified by segmentations from a deep convolutional neural network. Compared to control mice, the total dentate gyrus volume doubled and the granular layer volume quadrupled 21 days after injecting kainate. Subsequent sectioning of the same mouse brains allowed for benchmarking 3D X-ray histology against well-established histochemical and immunofluorescence stainings. Thus, 3D X-ray histology is a complementary neuroimaging tool to unlock the third dimension for the cellular-resolution histopathological analysis of mTLE.
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Affiliation(s)
- Griffin Rodgers
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
- Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland
| | - Christos Bikis
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
- Integrierte Psychiatrie Winterthur-Zürcher Unterland, 8408 Winterthur, Switzerland
| | - Philipp Janz
- Faculty of Medicine, Experimental Epilepsy Research, Department of Neurosurgery, Medical Center-University of Freiburg, 79106 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79106 Freiburg, Germany
- BrainLinks-BrainTools Center, University of Freiburg, 79106 Freiburg, Germany
| | - Christine Tanner
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
- Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland
| | - Georg Schulz
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
- Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland
- Core Facility Micro- and Nanotomography, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
| | - Peter Thalmann
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
| | - Carola A Haas
- Faculty of Medicine, Experimental Epilepsy Research, Department of Neurosurgery, Medical Center-University of Freiburg, 79106 Freiburg, Germany
- BrainLinks-BrainTools Center, University of Freiburg, 79106 Freiburg, Germany
- Center of Basics in NeuroModulation, Faculty of Medicine, University of Freiburg, 79114 Freiburg, Germany
| | - Bert Müller
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
- Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland
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4
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Flenner S, Hagemann J, Wittwer F, Longo E, Kubec A, Rothkirch A, David C, Müller M, Greving I. Hard X-ray full-field nanoimaging using a direct photon-counting detector. JOURNAL OF SYNCHROTRON RADIATION 2023; 30:390-399. [PMID: 36891852 PMCID: PMC10000802 DOI: 10.1107/s1600577522012103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
Full-field X-ray nanoimaging is a widely used tool in a broad range of scientific areas. In particular, for low-absorbing biological or medical samples, phase contrast methods have to be considered. Three well established phase contrast methods at the nanoscale are transmission X-ray microscopy with Zernike phase contrast, near-field holography and near-field ptychography. The high spatial resolution, however, often comes with the drawback of a lower signal-to-noise ratio and significantly longer scan times, compared with microimaging. In order to tackle these challenges a single-photon-counting detector has been implemented at the nanoimaging endstation of the beamline P05 at PETRA III (DESY, Hamburg) operated by Helmholtz-Zentrum Hereon. Thanks to the long sample-to-detector distance available, spatial resolutions of below 100 nm were reached in all three presented nanoimaging techniques. This work shows that a single-photon-counting detector in combination with a long sample-to-detector distance allows one to increase the time resolution for in situ nanoimaging, while keeping a high signal-to-noise level.
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Affiliation(s)
- Silja Flenner
- Helmholtz-Zentrum Hereon, Max-Planck-Strasse 1, 21502 Geesthacht, Germany
| | - Johannes Hagemann
- Center for X-ray and Nano Science – CXNS, Deutsches Elektronen-Synchrotron – DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Felix Wittwer
- Center for X-ray and Nano Science – CXNS, Deutsches Elektronen-Synchrotron – DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Elena Longo
- Helmholtz-Zentrum Hereon, Max-Planck-Strasse 1, 21502 Geesthacht, Germany
| | - Adam Kubec
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - André Rothkirch
- Center for X-ray and Nano Science – CXNS, Deutsches Elektronen-Synchrotron – DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Christian David
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Martin Müller
- Helmholtz-Zentrum Hereon, Max-Planck-Strasse 1, 21502 Geesthacht, Germany
| | - Imke Greving
- Helmholtz-Zentrum Hereon, Max-Planck-Strasse 1, 21502 Geesthacht, Germany
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5
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Busse M, Ferstl S, Kimm MA, Hehn L, Steiger K, Allner S, Muller M, Drecoll E, Burkner T, Dierolf M, Gleich B, Weichert W, Pfeiffer F. Multi-Scale Investigation of Human Renal Tissue in Three Dimensions. IEEE TRANSACTIONS ON MEDICAL IMAGING 2022; 41:3489-3497. [PMID: 36251918 DOI: 10.1109/tmi.2022.3214344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Histopathology as a diagnostic mainstay for tissue evaluation is strictly a 2D technology. Combining and supplementing this technology with 3D imaging has been proposed as one future avenue towards refining comprehensive tissue analysis. To this end, we have developed a laboratory-based X-ray method allowing for the investigation of tissue samples in three dimensions with isotropic volume information. To assess the potential of our method for micro-morphology evaluation, we selected several kidney regions from three patients with cystic kidney disease, obstructive nephropathy and diabetic glomerulopathy. Tissue specimens were processed using our in-house-developed X-ray eosin stain and investigated with a commercial microCT and our in-house-built NanoCT. The microCT system provided overview scans with voxel sizes of [Formula: see text] and the NanoCT was employed for higher resolutions including voxel sizes from [Formula: see text] to 210 nm. We present a methodology allowing for a precise micro-morphologic investigation in three dimensions which is compatible with conventional histology. Advantages of our methodology are its versatility with respect to multi-scale investigations, being laboratory-based, allowing for non-destructive imaging and providing isotropic volume information. We believe, that after future developmental work this method might contribute to advanced multi-modal tissue diagnostics.
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6
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Handschuh S, Okada CTC, Walter I, Aurich C, Glösmann M. An optimized workflow for
microCT
imaging of formalin‐fixed and paraffin‐embedded (
FFPE
) early equine embryos. Anat Histol Embryol 2022; 51:611-623. [PMID: 35851500 PMCID: PMC9542120 DOI: 10.1111/ahe.12834] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 07/01/2022] [Indexed: 01/14/2023]
Abstract
Here, we describe a workflow for high‐detail microCT imaging of formalin‐fixed and paraffin‐embedded (FFPE) equine embryos recovered on Day 34 of pregnancy (E34), a period just before placenta formation. The presented imaging methods are suitable for large animals' embryos with intention to study morphological and developmental aspects, but more generally can be adopted for all kinds of FFPE tissue specimens. Microscopic 3D imaging techniques such as microCT are important tools for detecting and studying normal embryogenesis and developmental disorders. To date, microCT imaging of vertebrate embryos was mostly done on embryos that have been stained with an X‐ray dense contrast agent. Here, we describe an alternative imaging procedure that allows to visualize embryo morphology and organ development in unstained FFPE embryos. Two aspects are critical for high‐quality data acquisition: (i) a proper sample mounting leaving as little as possible paraffin around the sample and (ii) an image filtering pipeline that improves signal‐to‐noise ratio in these inherently low‐contrast data sets. The presented workflow allows overview imaging of the whole embryo proper and can be used for determination of organ volumes and development. Furthermore, we show that high‐resolution interior tomographies can provide virtual histology information from selected regions of interest. In addition, we demonstrate that microCT scanned embryos remain intact during the scanning procedure allowing for a subsequent investigation by routine histology and/or immunohistochemistry. This makes the presented workflow applicable also to archival paraffin‐embedded material.
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Affiliation(s)
- Stephan Handschuh
- VetCore Facility for Research/Imaging Unit University of Veterinary Medicine Vienna Vienna Austria
| | - Carolina T. C. Okada
- Platform Artificial Insemination and Embryo Transfer Department for Small Animals and Horses University of Veterinary Medicine Vienna Vienna Austria
| | - Ingrid Walter
- VetCore Facility for Research/VetBiobank University of Veterinary Medicine Vienna Vienna Austria
- Institute of Morphology University of Veterinary Medicine Vienna Vienna Austria
| | - Christine Aurich
- Platform Artificial Insemination and Embryo Transfer Department for Small Animals and Horses University of Veterinary Medicine Vienna Vienna Austria
| | - Martin Glösmann
- VetCore Facility for Research/Imaging Unit University of Veterinary Medicine Vienna Vienna Austria
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7
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Kunishima N, Hirose R, Takeda Y, Ito K, Furuichi K, Omote K. Nondestructive cellular-level 3D observation of mouse kidney using laboratory-based X-ray microscopy with paraffin-mediated contrast enhancement. Sci Rep 2022; 12:9436. [PMID: 35676517 PMCID: PMC9177607 DOI: 10.1038/s41598-022-13394-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 05/13/2022] [Indexed: 11/26/2022] Open
Abstract
For three-dimensional observation of unstained bio-specimens using X-ray microscopy with computed tomography (CT), one main problem has been low contrast in X-ray absorption. Here we introduce paraffin-mediated contrast enhancement to visualize biopsy samples of mouse kidney using a laboratory-based X-tray microscope. Unlike conventional heavy-atom staining, paraffin-mediated contrast enhancement uses solid paraffin as a negative contrast medium to replace water in the sample. The medium replacement from water to paraffin effectively lowers the absorption of low-energy X-rays by the medium, which eventually enhances the absorption contrast between the medium and tissue. In this work, paraffin-mediated contrast enhancement with 8 keV laboratory X-rays was used to visualize cylindrical renal biopsies with diameters of about 0.5 mm. As a result, reconstructed CT images from 19.4 h of data collection achieved cellular-level resolutions in all directions, which provided 3D structures of renal corpuscles from a normal mouse and from a disease model mouse. These two structures with and without disease allowed a volumetric analysis showing substantial volume differences in glomerular subregions. Notably, this nondestructive method presents CT opacities reflecting elemental composition and density of unstained tissues, thereby allowing more unbiased interpretation on their biological structures.
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8
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Vogl C, Neef J, Wichmann C. Methods for multiscale structural and functional analysis of the mammalian cochlea. Mol Cell Neurosci 2022; 120:103720. [DOI: 10.1016/j.mcn.2022.103720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 02/13/2022] [Accepted: 03/08/2022] [Indexed: 01/11/2023] Open
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9
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Chourrout M, Rositi H, Ong E, Hubert V, Paccalet A, Foucault L, Autret A, Fayard B, Olivier C, Bolbos R, Peyrin F, Crola-da-Silva C, Meyronet D, Raineteau O, Elleaume H, Brun E, Chauveau F, Wiart M. Brain virtual histology with X-ray phase-contrast tomography Part I: whole-brain myelin mapping in white-matter injury models. BIOMEDICAL OPTICS EXPRESS 2022; 13:1620-1639. [PMID: 35415001 PMCID: PMC8973191 DOI: 10.1364/boe.438832] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/08/2021] [Accepted: 11/02/2021] [Indexed: 06/14/2023]
Abstract
White-matter injury leads to severe functional loss in many neurological diseases. Myelin staining on histological samples is the most common technique to investigate white-matter fibers. However, tissue processing and sectioning may affect the reliability of 3D volumetric assessments. The purpose of this study was to propose an approach that enables myelin fibers to be mapped in the whole rodent brain with microscopic resolution and without the need for strenuous staining. With this aim, we coupled in-line (propagation-based) X-ray phase-contrast tomography (XPCT) to ethanol-induced brain sample dehydration. We here provide the proof-of-concept that this approach enhances myelinated axons in rodent and human brain tissue. In addition, we demonstrated that white-matter injuries could be detected and quantified with this approach, using three animal models: ischemic stroke, premature birth and multiple sclerosis. Furthermore, in analogy to diffusion tensor imaging (DTI), we retrieved fiber directions and DTI-like diffusion metrics from our XPCT data to quantitatively characterize white-matter microstructure. Finally, we showed that this non-destructive approach was compatible with subsequent complementary brain sample analysis by conventional histology. In-line XPCT might thus become a novel gold-standard for investigating white-matter injury in the intact brain. This is Part I of a series of two articles reporting the value of in-line XPCT for virtual histology of the brain; Part II shows how in-line XPCT enables the whole-brain 3D morphometric analysis of amyloid- β (A β ) plaques.
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Affiliation(s)
- Matthieu Chourrout
- Univ-Lyon, Lyon Neuroscience
Research Center, CNRS UMR5292, Inserm U1028,
Université Claude Bernard Lyon 1, Lyon, France
- Co-first authors
| | - Hugo Rositi
- Univ-Clermont Auvergne; CNRS;
SIGMA Clermont; Institut Pascal,
Clermont-Ferrand, France
- Co-first authors
| | - Elodie Ong
- Univ-Lyon, CarMeN
laboratory, Inserm U1060, INRA U1397, Université
Claude Bernard Lyon 1, INSA Lyon, Charles Mérieux Medical
School, F-69600, Oullins, France
- Univ-Lyon, Hospices Civils de
Lyon, Lyon, France
| | - Violaine Hubert
- Univ-Lyon, CarMeN
laboratory, Inserm U1060, INRA U1397, Université
Claude Bernard Lyon 1, INSA Lyon, Charles Mérieux Medical
School, F-69600, Oullins, France
| | - Alexandre Paccalet
- Univ-Lyon, CarMeN
laboratory, Inserm U1060, INRA U1397, Université
Claude Bernard Lyon 1, INSA Lyon, Charles Mérieux Medical
School, F-69600, Oullins, France
| | - Louis Foucault
- Univ-Lyon, Université
Claude Bernard Lyon 1, Inserm, Stem Cell and Brain
Research Institute U1208, 69500 Bron, France
| | | | | | - Cécile Olivier
- Univ-Lyon, INSA-Lyon,
Université Claude Bernard Lyon 1,
CNRS, Inserm, CREATIS UMR5220, U1206, F-69621, France
| | | | - Françoise Peyrin
- Univ-Lyon, INSA-Lyon,
Université Claude Bernard Lyon 1,
CNRS, Inserm, CREATIS UMR5220, U1206, F-69621, France
| | - Claire Crola-da-Silva
- Univ-Lyon, CarMeN
laboratory, Inserm U1060, INRA U1397, Université
Claude Bernard Lyon 1, INSA Lyon, Charles Mérieux Medical
School, F-69600, Oullins, France
| | | | - Olivier Raineteau
- Univ-Lyon, Université
Claude Bernard Lyon 1, Inserm, Stem Cell and Brain
Research Institute U1208, 69500 Bron, France
| | - Héléne Elleaume
- Université Grenoble
Alpes, Inserm UA7 Strobe, Grenoble, France
| | - Emmanuel Brun
- Université Grenoble
Alpes, Inserm UA7 Strobe, Grenoble, France
| | - Fabien Chauveau
- Univ-Lyon, Lyon Neuroscience
Research Center, CNRS UMR5292, Inserm U1028,
Université Claude Bernard Lyon 1, Lyon, France
- CNRS, Lyon,
France
- Co-last authors
| | - Marlene Wiart
- Univ-Lyon, CarMeN
laboratory, Inserm U1060, INRA U1397, Université
Claude Bernard Lyon 1, INSA Lyon, Charles Mérieux Medical
School, F-69600, Oullins, France
- CNRS, Lyon,
France
- Co-last authors
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10
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Rodgers G, Tanner C, Schulz G, Migga A, Kuo W, Bikis C, Scheel M, Kurtcuoglu V, Weitkamp T, Müller B. Virtual histology of an entire mouse brain from formalin fixation to paraffin embedding. Part 2: Volumetric strain fields and local contrast changes. J Neurosci Methods 2022; 365:109385. [PMID: 34637810 DOI: 10.1016/j.jneumeth.2021.109385] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/07/2021] [Indexed: 01/14/2023]
Abstract
BACKGROUND Fixation and embedding of post mortem brain tissue is a pre-requisite for both gold-standard conventional histology and X-ray virtual histology. This process alters the morphology and density of the brain microanatomy. NEW METHOD To quantify these changes, we employed synchrotron radiation-based hard X-ray tomography with 3 μm voxel length to visualize the same mouse brain after fixation in 4% formalin, immersion in ethanol solutions (50%, 70%, 80%, 90%, and 100%), xylene, and finally after embedding in a paraffin block. The volumetric data were non-rigidly registered to the initial formalin-fixed state to align the microanatomy within the entire mouse brain. RESULTS Volumetric strain fields were used to characterize local shrinkage, which was found to depend on the anatomical region and distance to external surface. X-ray contrast was altered and enhanced by preparation-induced inter-tissue density changes. The preparation step can be selected to highlight specific anatomical features. For example, fiber tract contrast is amplified in 100% ethanol. COMPARISON WITH EXISTING METHODS Our method provides volumetric strain fields, unlike approaches based on feature-to-feature or volume measurements. Volumetric strain fields are produced by non-rigid registration, which is less labor-intensive and observer-dependent than volume change measurements based on manual segmentations. X-ray microtomography provides spatial resolution at least an order of magnitude higher than magnetic resonance microscopy, allowing for analysis of morphology and density changes within the brain's microanatomy. CONCLUSION Our approach belongs to three-dimensional virtual histology with isotropic micrometer spatial resolution and therefore complements atlases based on a combination of magnetic resonance microscopy and optical micrographs of serial histological sections.
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Affiliation(s)
- Griffin Rodgers
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland; Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland
| | - Christine Tanner
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland; Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland.
| | - Georg Schulz
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland; Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland
| | - Alexandra Migga
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland; Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland
| | - Willy Kuo
- The Interface Group, Institute of Physiology, University of Zurich, 8057 Zurich, Switzerland; National Centre of Competence in Research, Kidney.CH, 8057 Zurich, Switzerland
| | - Christos Bikis
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland; Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland; Integrierte Psychiatrie Winterthur - Zürcher Unterland, 8408 Winterthur, Switzerland
| | - Mario Scheel
- Synchrotron Soleil, 91192 Gif-sur-Yvette, France
| | - Vartan Kurtcuoglu
- The Interface Group, Institute of Physiology, University of Zurich, 8057 Zurich, Switzerland; National Centre of Competence in Research, Kidney.CH, 8057 Zurich, Switzerland
| | | | - Bert Müller
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland; Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland
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11
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Eckermann M, van der Meer F, Cloetens P, Ruhwedel T, Möbius W, Stadelmann C, Salditt T. Three-dimensional virtual histology of the cerebral cortex based on phase-contrast X-ray tomography. BIOMEDICAL OPTICS EXPRESS 2021; 12:7582-7598. [PMID: 35003854 PMCID: PMC8713656 DOI: 10.1364/boe.434885] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 05/09/2023]
Abstract
In this work, we optimize the setups and experimental parameters of X-ray phase-contrast computed-tomography for the three-dimensional imaging of the cyto- and myeloarchitecture of cerebral cortex, including both human and murine tissue. We present examples for different optical configurations using state-of-the art synchrotron instruments for holographic tomography, as well as compact laboratory setups for phase-contrast tomography in the direct contrast (edge-enhancement) regime. Apart from unstained and paraffin-embedded tissue, we tested hydrated tissue, as well as heavy metal stained and resin-embedded tissue using two different protocols. Further, we show that the image quality achieved allows to assess the neuropathology of multiple sclerosis in a biopsy sample collected during surgery.
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Affiliation(s)
- Marina Eckermann
- Institut für Röntgenphysik, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
| | | | - Peter Cloetens
- ESRF, the European Synchrotron, 71, avenue des Martyrs, 38043 Grenoble Cedex 9, France
| | - Torben Ruhwedel
- Max-Planck-Institut für experimentelle Medizin, Hermann-Rein-Straße 3, 37075 Göttingen, Germany
| | - Wiebke Möbius
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
- Max-Planck-Institut für experimentelle Medizin, Hermann-Rein-Straße 3, 37075 Göttingen, Germany
| | - Christine Stadelmann
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
- Institut für Neuropathologie, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Tim Salditt
- Institut für Röntgenphysik, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
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12
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Virtual histology of an entire mouse brain from formalin fixation to paraffin embedding. Part 1: Data acquisition, anatomical feature segmentation, tracking global volume and density changes. J Neurosci Methods 2021; 364:109354. [PMID: 34529981 DOI: 10.1016/j.jneumeth.2021.109354] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/01/2021] [Accepted: 09/04/2021] [Indexed: 01/14/2023]
Abstract
BACKGROUND Micrometer-resolution neuroimaging with gold-standard conventional histology requires tissue fixation and embedding. The exchange of solvents for the creation of sectionable paraffin blocks modifies tissue density and generates non-uniform brain shrinkage. NEW METHOD We employed synchrotron radiation-based X-ray microtomography for slicing- and label-free virtual histology of the mouse brain at different stages of the standard preparation protocol from formalin fixation via ascending ethanol solutions and xylene to paraffin embedding. Segmentation of anatomical regions allowed us to quantify non-uniform tissue shrinkage. Global and local changes in X-ray absorption gave insight into contrast enhancement for virtual histology. RESULTS The volume of the entire mouse brain was 60%, 56%, and 40% of that in formalin for, respectively, 100% ethanol, xylene, and paraffin. The volume changes of anatomical regions such as the hippocampus, anterior commissure, and ventricles differ from the global volume change. X-ray absorption of the full brain decreased, while local absorption differences increased, resulting in enhanced contrast for virtual histology. These trends were also observed with laboratory microtomography measurements. COMPARISON WITH EXISTING METHODS Microtomography provided sub-10 μm spatial resolution with sufficient density resolution to resolve anatomical structures at each step of the embedding protocol. The spatial resolution of conventional computed tomography and magnetic resonance microscopy is an order of magnitude lower and both do not match the contrast of microtomography over the entire embedding protocol. Unlike feature-to-feature or total volume measurements, our approach allows for calculation of volume change based on segmentation. CONCLUSION We present isotropic micrometer-resolution imaging to quantify morphology and composition changes in a mouse brain during the standard histological preparation. The proposed method can be employed to identify the most appropriate embedding medium for anatomical feature visualization, to reveal the basis for the dramatic X-ray contrast enhancement observed in numerous embedded tissues, and to quantify morphological changes during tissue fixation and embedding.
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13
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Liimatainen K, Latonen L, Valkonen M, Kartasalo K, Ruusuvuori P. Virtual reality for 3D histology: multi-scale visualization of organs with interactive feature exploration. BMC Cancer 2021; 21:1133. [PMID: 34686173 PMCID: PMC8539837 DOI: 10.1186/s12885-021-08542-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 06/29/2021] [Indexed: 11/23/2022] Open
Abstract
Background Virtual reality (VR) enables data visualization in an immersive and engaging manner, and it can be used for creating ways to explore scientific data. Here, we use VR for visualization of 3D histology data, creating a novel interface for digital pathology to aid cancer research. Methods Our contribution includes 3D modeling of a whole organ and embedded objects of interest, fusing the models with associated quantitative features and full resolution serial section patches, and implementing the virtual reality application. Our VR application is multi-scale in nature, covering two object levels representing different ranges of detail, namely organ level and sub-organ level. In addition, the application includes several data layers, including the measured histology image layer and multiple representations of quantitative features computed from the histology. Results In our interactive VR application, the user can set visualization properties, select different samples and features, and interact with various objects, which is not possible in the traditional 2D-image view used in digital pathology. In this work, we used whole mouse prostates (organ level) with prostate cancer tumors (sub-organ objects of interest) as example cases, and included quantitative histological features relevant for tumor biology in the VR model. Conclusions Our application enables a novel way for exploration of high-resolution, multidimensional data for biomedical research purposes, and can also be used in teaching and researcher training. Due to automated processing of the histology data, our application can be easily adopted to visualize other organs and pathologies from various origins. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08542-9.
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Affiliation(s)
- Kaisa Liimatainen
- Faculty of Medicine and Health Technology, Tampere University, FI-33014, Tampere, Finland
| | - Leena Latonen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Masi Valkonen
- Faculty of Medicine and Health Technology, Tampere University, FI-33014, Tampere, Finland
| | - Kimmo Kartasalo
- Faculty of Medicine and Health Technology, Tampere University, FI-33014, Tampere, Finland
| | - Pekka Ruusuvuori
- Faculty of Medicine and Health Technology, Tampere University, FI-33014, Tampere, Finland. .,Cancer Research Unit and FICAN West Cancer Centre, Institute of Biomedicine, University of Turku and Turku University Hospital, FI-20014, Turku, Finland.
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14
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Pierantoni M, Silva Barreto I, Hammerman M, Verhoeven L, Törnquist E, Novak V, Mokso R, Eliasson P, Isaksson H. A quality optimization approach to image Achilles tendon microstructure by phase-contrast enhanced synchrotron micro-tomography. Sci Rep 2021; 11:17313. [PMID: 34453067 PMCID: PMC8397765 DOI: 10.1038/s41598-021-96589-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 08/06/2021] [Indexed: 12/19/2022] Open
Abstract
Achilles tendons are mechanosensitive, and their complex hierarchical structure is in part the result of the mechanical stimulation conveyed by the muscles. To fully understand how their microstructure responds to mechanical loading a non-invasive approach for 3D high resolution imaging suitable for soft tissue is required. Here we propose a protocol that can capture the complex 3D organization of the Achilles tendon microstructure, using phase-contrast enhanced synchrotron micro-tomography (SR-PhC-μCT). We investigate the effects that sample preparation and imaging conditions have on the resulting image quality, by considering four types of sample preparations and two imaging setups (sub-micrometric and micrometric final pixel sizes). The image quality is assessed using four quantitative parameters. The results show that for studying tendon collagen fibers, conventional invasive sample preparations such as fixation and embedding are not necessary or advantageous. Instead, fresh frozen samples result in high-quality images that capture the complex 3D organization of tendon fibers in conditions as close as possible to natural. The comprehensive nature of this innovative study by SR-PhC-μCT breaks ground for future studies of soft complex biological tissue in 3D with high resolution in close to natural conditions, which could be further used for in situ characterization of how soft tissue responds to mechanical stimuli on a microscopic level.
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Affiliation(s)
- Maria Pierantoni
- Department of Biomedical Engineering, Lund University, Box 118, 221 00, Lund, Sweden.
| | | | - Malin Hammerman
- Department of Biomedical Engineering, Lund University, Box 118, 221 00, Lund, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, 581 83, Linköping, Sweden
| | - Lissa Verhoeven
- Department of Biomedical Engineering, Lund University, Box 118, 221 00, Lund, Sweden
| | - Elin Törnquist
- Department of Biomedical Engineering, Lund University, Box 118, 221 00, Lund, Sweden
| | - Vladimir Novak
- Swiss Light Source, Paul Scherrer Institute, 5232, Villigen, Switzerland
| | - Rajmund Mokso
- Swiss Light Source, Paul Scherrer Institute, 5232, Villigen, Switzerland
- Division of Solid Mechanics, Lund University, Box 118, 221 00, Lund, Sweden
| | - Pernilla Eliasson
- Department of Biomedical and Clinical Sciences, Linköping University, 581 83, Linköping, Sweden
| | - Hanna Isaksson
- Department of Biomedical Engineering, Lund University, Box 118, 221 00, Lund, Sweden
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15
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Simultaneous 3D Visualization of the Microvascular and Neural Network in Mouse Spinal Cord Using Synchrotron Radiation Micro-Computed Tomography. Neurosci Bull 2021; 37:1469-1480. [PMID: 34146232 PMCID: PMC8490558 DOI: 10.1007/s12264-021-00715-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 02/06/2021] [Indexed: 11/01/2022] Open
Abstract
Effective methods for visualizing neurovascular morphology are essential for understanding the normal spinal cord and the morphological alterations associated with diseases. However, ideal techniques for simultaneously imaging neurovascular structure in a broad region of a specimen are still lacking. In this study, we combined Golgi staining with angiography and synchrotron radiation micro-computed tomography (SRμCT) to visualize the 3D neurovascular network in the mouse spinal cord. Using our method, the 3D neurons, nerve fibers, and vasculature in a broad region could be visualized in the same image at cellular resolution without destructive sectioning. Besides, we found that the 3D morphology of neurons, nerve fiber tracts, and vasculature visualized by SRμCT were highly consistent with that visualized using the histological method. Moreover, the 3D neurovascular structure could be quantitatively evaluated by the combined methodology. The method shown here will be useful in fundamental neuroscience studies.
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16
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Three-Dimensional X-ray Imaging of β-Galactosidase Reporter Activity by Micro-CT: Implication for Quantitative Analysis of Gene Expression. Brain Sci 2021; 11:brainsci11060746. [PMID: 34199780 PMCID: PMC8230009 DOI: 10.3390/brainsci11060746] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 02/07/2023] Open
Abstract
Acquisition of detailed anatomical and molecular knowledge from intact biological samples while preserving their native three-dimensional structure is still a challenging issue for imaging studies aiming to unravel a system's functions. Three-dimensional micro-CT X-ray imaging with a high spatial resolution in minimally perturbed naive non-transparent samples has recently gained increased popularity and broad application in biomedical research. Here, we describe a novel X-ray-based methodology for analysis of β-galactosidase (lacZ) reporter-driven gene expression in an intact murine brain ex vivo by micro-CT. The method relies on detection of bromine molecules in the product of the enzymatic β-galactosidase reaction. Enhancement of the X-ray signal is observed specifically in the regions of the murine brain where expression of the lacZ reporter gene is also detected histologically. We performed quantitative analysis of the expression levels of lacZ reporter activity by relative radiodensity estimation of the β-galactosidase/X-gal precipitate in situ. To demonstrate the feasibility of the method, we performed expression analysis of the Tsen54-lacZ reporter gene in the murine brain in a semi-quantitative manner. Human mutations in the Tsen54 gene cause pontocerebellar hypoplasia (PCH), a group of severe neurodegenerative disorders with both mental and motor deficits. Comparing relative levels of Tsen54 gene expression, we demonstrate that the highest Tsen54 expression is observed in anatomical brain substructures important for the normal motor and memory functions in mice.
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17
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Keppeler D, Kampshoff CA, Thirumalai A, Duque-Afonso CJ, Schaeper JJ, Quilitz T, Töpperwien M, Vogl C, Hessler R, Meyer A, Salditt T, Moser T. Multiscale photonic imaging of the native and implanted cochlea. Proc Natl Acad Sci U S A 2021; 118:e2014472118. [PMID: 33903231 PMCID: PMC8106341 DOI: 10.1073/pnas.2014472118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The cochlea of our auditory system is an intricate structure deeply embedded in the temporal bone. Compared with other sensory organs such as the eye, the cochlea has remained poorly accessible for investigation, for example, by imaging. This limitation also concerns the further development of technology for restoring hearing in the case of cochlear dysfunction, which requires quantitative information on spatial dimensions and the sensorineural status of the cochlea. Here, we employed X-ray phase-contrast tomography and light-sheet fluorescence microscopy and their combination for multiscale and multimodal imaging of cochlear morphology in species that serve as established animal models for auditory research. We provide a systematic reference for morphological parameters relevant for cochlear implant development for rodent and nonhuman primate models. We simulate the spread of light from the emitters of the optical implants within the reconstructed nonhuman primate cochlea, which indicates a spatially narrow optogenetic excitation of spiral ganglion neurons.
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Affiliation(s)
- Daniel Keppeler
- Institute for Auditory Neuroscience, University Medical Center Göttingen, 37075 Göttingen, Germany
- InnerEarLab, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Christoph A Kampshoff
- Institute for Auditory Neuroscience, University Medical Center Göttingen, 37075 Göttingen, Germany
- InnerEarLab, University Medical Center Göttingen, 37075 Göttingen, Germany
- Department of Otolaryngology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Anupriya Thirumalai
- Institute for Auditory Neuroscience, University Medical Center Göttingen, 37075 Göttingen, Germany
- InnerEarLab, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Carlos J Duque-Afonso
- Institute for Auditory Neuroscience, University Medical Center Göttingen, 37075 Göttingen, Germany
- InnerEarLab, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Jannis J Schaeper
- Institute for X-ray Physics, University of Göttingen, 37075 Göttingen, Germany
| | - Tabea Quilitz
- Institute for Auditory Neuroscience, University Medical Center Göttingen, 37075 Göttingen, Germany
- InnerEarLab, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Mareike Töpperwien
- Institute for X-ray Physics, University of Göttingen, 37075 Göttingen, Germany
| | - Christian Vogl
- Institute for Auditory Neuroscience, University Medical Center Göttingen, 37075 Göttingen, Germany
- InnerEarLab, University Medical Center Göttingen, 37075 Göttingen, Germany
| | | | - Alexander Meyer
- InnerEarLab, University Medical Center Göttingen, 37075 Göttingen, Germany
- Department of Otolaryngology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Tim Salditt
- Institute for X-ray Physics, University of Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells," University of Göttingen, 37075 Göttingen, Germany
| | - Tobias Moser
- Institute for Auditory Neuroscience, University Medical Center Göttingen, 37075 Göttingen, Germany;
- InnerEarLab, University Medical Center Göttingen, 37075 Göttingen, Germany
- Department of Otolaryngology, University Medical Center Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells," University of Göttingen, 37075 Göttingen, Germany
- Auditory Neuroscience and Optogenetics Laboratory, German Primate Center, 37075 Göttingen, Germany
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18
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Frohn J, Pinkert-Leetsch D, Missbach-Güntner J, Reichardt M, Osterhoff M, Alves F, Salditt T. 3D virtual histology of human pancreatic tissue by multiscale phase-contrast X-ray tomography. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:1707-1719. [PMID: 33147198 PMCID: PMC7642968 DOI: 10.1107/s1600577520011327] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/18/2020] [Indexed: 05/05/2023]
Abstract
A multiscale three-dimensional (3D) virtual histology approach is presented, based on two configurations of propagation phase-contrast X-ray tomography, which have been implemented in close proximity at the GINIX endstation at the beamline P10/PETRA III (DESY, Hamburg, Germany). This enables the 3D reconstruction of characteristic morphological features of human pancreatic normal and tumor tissue, as obtained from cancer surgery, first in the form of a large-scale overview by parallel-beam illumination, followed by a zoom into a region-of-interest based on zoom tomography using a Kirkpatrick-Baez mirror with additional waveguide optics. To this end 1 mm punch biopsies of the tissue were taken. In the parallel tomography, a volumetric throughput on the order of 0.01 mm3 s-1 was achieved, while maintaining the ability to segment isolated cells. With a continuous rotation during the scan, a total acquisition time of less than 2 min was required for a full tomographic scan. Using the combination of both setups, islets of Langerhans, a three-dimensional cluster of cells in the endocrine part of the pancreas, could be located. Cells in such an islet were segmented and visualized in 3D. Further, morphological alterations of tumorous tissue of the pancreas were characterized. To this end, the anisotropy parameter Ω, based on intensity gradients, was used in order to quantify the presence of collagen fibers within the entire biopsy specimen. This proof-of-concept experiment of the multiscale approach on human pancreatic tissue paves the way for future 3D virtual pathology.
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Affiliation(s)
- Jasper Frohn
- Institute for X-ray Physics, Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Diana Pinkert-Leetsch
- Institute of Diagnostic and Interventional Radiology, University Medical Center Göttingen, Robert Koch Strasse 40, 37075 Göttingen, Germany
- Max Planck Institute for Experimental Medicine, Group of Translational Molecular Imaging, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
| | - Jeannine Missbach-Güntner
- Institute of Diagnostic and Interventional Radiology, University Medical Center Göttingen, Robert Koch Strasse 40, 37075 Göttingen, Germany
| | - Marius Reichardt
- Institute for X-ray Physics, Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Markus Osterhoff
- Institute for X-ray Physics, Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Frauke Alves
- Institute of Diagnostic and Interventional Radiology, University Medical Center Göttingen, Robert Koch Strasse 40, 37075 Göttingen, Germany
- Max Planck Institute for Experimental Medicine, Group of Translational Molecular Imaging, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
- Clinic of Hematology and Medical Oncology, University Medical Center Göttingen, Robert Koch Strase 40, 37075 Göttingen, Germany
| | - Tim Salditt
- Institute for X-ray Physics, Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
- Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells (MBExC), University Medical Center Göttingen, Robert Koch Strase 40, 37075 Göttingen, Germany
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19
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Peruzzi N, Veress B, Dahlin LB, Salditt T, Andersson M, Eckermann M, Frohn J, Robisch AL, Bech M, Ohlsson B. 3D analysis of the myenteric plexus of the human bowel by X-ray phase-contrast tomography - a future method? Scand J Gastroenterol 2020; 55:1261-1267. [PMID: 32907418 DOI: 10.1080/00365521.2020.1815079] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVES Light microscopical analysis in two dimensions, combined with immunohistochemistry, is presently the gold standard to describe the enteric nervous system (ENS). Our aim was to assess the usefulness of three-dimensional (3D) imaging by X-ray phase-contrast tomography in evaluating the ENS of the human bowel. MATERIAL AND METHODS Myenteric ganglia were identified in full-thickness biopsies of the ileum and colon by hematoxylin & eosin staining. A1-mm biopsy punch was taken from the paraffin blocks and placed into a Kapton® tube for subsequent tomographic investigation. The samples were scanned, without further preparation, using phase-contrast tomography at two different scales: overview scans (performed with laboratory setups), which allowed localization of the nervous tissue (∼1µm effective voxel size); and high-resolution scans (performed with a synchrotron endstation), which imaged localized regions of 320x320x320 µm3 (176 nm effective voxel size). RESULTS The contrast allowed us to follow the shape and the size changes of the ganglia, as well as to study their cellular components together with the cells and cellular projections of the periganglional space. Furthermore, it was possible to show the 3D network of the myenteric plexus and to quantify its volume within the samples. CONCLUSIONS Phase-contrast X-ray tomography can be applied for volume analyses of the human ENS and to study tissue components in unstained paraffin-embedded tissue biopsies. This technique could potentially be used to study disease mechanisms, and to compare healthy and diseased tissues in clinical research.
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Affiliation(s)
- Niccolò Peruzzi
- Division of Medical Radiation Physics, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Béla Veress
- Department of Pathology, Skåne University Hospital, Malmö, Sweden
| | - Lars B Dahlin
- Department of Translational Medicine - Hand Surgery, Lund University, Malmö, Sweden.,Department of Hand Surgery, Skåne University Hospital, Malmö, Sweden
| | - Tim Salditt
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
| | - Mariam Andersson
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Lyngby, Denmark.,Danish Research Centre for Magnetic Resonance (DRCMR), Center for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
| | - Marina Eckermann
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
| | - Jasper Frohn
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany
| | - Anna-Lena Robisch
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany
| | - Martin Bech
- Division of Medical Radiation Physics, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Bodil Ohlsson
- Lund University, Skåne University Hospital, Department of Internal Medicine, Malmö, Sweden
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20
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Eckermann M, Frohn J, Reichardt M, Osterhoff M, Sprung M, Westermeier F, Tzankov A, Werlein C, Kühnel M, Jonigk D, Salditt T. 3D virtual pathohistology of lung tissue from Covid-19 patients based on phase contrast X-ray tomography. eLife 2020; 9:e60408. [PMID: 32815517 PMCID: PMC7473770 DOI: 10.7554/elife.60408] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/17/2020] [Indexed: 01/25/2023] Open
Abstract
We present a three-dimensional (3D) approach for virtual histology and histopathology based on multi-scale phase contrast x-ray tomography, and use this to investigate the parenchymal architecture of unstained lung tissue from patients who succumbed to Covid-19. Based on this first proof-of-concept study, we propose multi-scale phase contrast x-ray tomography as a tool to unravel the pathophysiology of Covid-19, extending conventional histology by a third dimension and allowing for full quantification of tissue remodeling. By combining parallel and cone beam geometry, autopsy samples with a maximum cross section of 8 mm are scanned and reconstructed at a resolution and image quality, which allows for the segmentation of individual cells. Using the zoom capability of the cone beam geometry, regions-of-interest are reconstructed with a minimum voxel size of 167 nm. We exemplify the capability of this approach by 3D visualization of diffuse alveolar damage (DAD) with its prominent hyaline membrane formation, by mapping the 3D distribution and density of lymphocytes infiltrating the tissue, and by providing histograms of characteristic distances from tissue interior to the closest air compartment.
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Affiliation(s)
- Marina Eckermann
- Institut für Röntgenphysik, Georg-August-UniversitätGöttingenGermany
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of GöttingenGöttingenGermany
| | - Jasper Frohn
- Institut für Röntgenphysik, Georg-August-UniversitätGöttingenGermany
| | - Marius Reichardt
- Institut für Röntgenphysik, Georg-August-UniversitätGöttingenGermany
| | - Markus Osterhoff
- Institut für Röntgenphysik, Georg-August-UniversitätGöttingenGermany
| | | | | | - Alexandar Tzankov
- Institut für Medizinische Genetik und Pathologie, Universitätsspital BaselBaselSwitzerland
| | - Christopher Werlein
- Medizinische Hochschule Hannover (MHH)HannoverGermany
- Deutsches Zentrum für Lungenforschung (DZL)Hannover (BREATH)Germany
| | - Mark Kühnel
- Medizinische Hochschule Hannover (MHH)HannoverGermany
- Deutsches Zentrum für Lungenforschung (DZL)Hannover (BREATH)Germany
| | - Danny Jonigk
- Medizinische Hochschule Hannover (MHH)HannoverGermany
- Deutsches Zentrum für Lungenforschung (DZL)Hannover (BREATH)Germany
| | - Tim Salditt
- Institut für Röntgenphysik, Georg-August-UniversitätGöttingenGermany
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of GöttingenGöttingenGermany
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21
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Barbone GE, Bravin A, Mittone A, Kraiger MJ, Hrabě de Angelis M, Bossi M, Ballarini E, Rodriguez-Menendez V, Ceresa C, Cavaletti G, Coan P. Establishing sample-preparation protocols for X-ray phase-contrast CT of rodent spinal cords: Aldehyde fixations and osmium impregnation. J Neurosci Methods 2020; 339:108744. [DOI: 10.1016/j.jneumeth.2020.108744] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 12/14/2022]
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22
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Reichardt M, Frohn J, Khan A, Alves F, Salditt T. Multi-scale X-ray phase-contrast tomography of murine heart tissue. BIOMEDICAL OPTICS EXPRESS 2020; 11:2633-2651. [PMID: 32499949 PMCID: PMC7249829 DOI: 10.1364/boe.386576] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/12/2020] [Accepted: 03/18/2020] [Indexed: 05/07/2023]
Abstract
The spatial organization of cardiac muscle tissue exhibits a complex structure on multiple length scales, from the sarcomeric unit to the whole organ. Here we demonstrate a multi-scale three-dimensional imaging (3d) approach with three levels of magnification, based on synchrotron X-ray phase contrast tomography. Whole mouse hearts are scanned in an undulator beam, which is first focused and then broadened by divergence. Regions-of-interest of the hearts are scanned in parallel beam as well as a biopsy by magnified cone beam geometry using a X-ray waveguide optic. Data is analyzed in terms of orientation, anisotropy and the sarcomeric periodicity via a local Fourier transformation.
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Affiliation(s)
- Marius Reichardt
- Gerorg-August-University, Institute for x-ray Physics, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Jasper Frohn
- Gerorg-August-University, Institute for x-ray Physics, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Amara Khan
- Max Planck Institute for Experimental Medicine, Group of Translational Molecular Imaging, German Hermann-Rein-Straße 3, 37075 Göttingen, Germany
| | - Frauke Alves
- Max Planck Institute for Experimental Medicine, Group of Translational Molecular Imaging, German Hermann-Rein-Straße 3, 37075 Göttingen, Germany
- University Medical Center Göttingen, Clinic of Hematology and Medical Oncology, Robert-Koch-Straße 40, 37075 Göttingen, Germany
- University Medical Center Göttingen, Institute for Diagnostic and Interventional Radiology, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Tim Salditt
- Gerorg-August-University, Institute for x-ray Physics, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
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Eckermann M, Töpperwien M, Robisch AL, van der Meer F, Stadelmann C, Salditt T. Phase-contrast x-ray tomography of neuronal tissue at laboratory sources with submicron resolution. J Med Imaging (Bellingham) 2020; 7:013502. [PMID: 32118088 PMCID: PMC7032481 DOI: 10.1117/1.jmi.7.1.013502] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 01/21/2020] [Indexed: 11/14/2022] Open
Abstract
Purpose: Recently, progress has been achieved in implementing phase-contrast tomography of soft biological tissues at laboratory sources. This opens up opportunities for three-dimensional (3-D) histology based on x-ray computed tomography (μ- and nanoCT) in the direct vicinity of hospitals and biomedical research institutions. Combining advanced x-ray generation and detection techniques with phase reconstruction algorithms, 3-D histology can be obtained even of unstained tissue of the central nervous system, as shown, for example, for biopsies and autopsies of human cerebellum. Depending on the setup, i.e., source, detector, and geometric parameters, laboratory-based tomography can be implemented at very different sizes and length scales. We investigate the extent to which 3-D histology of neuronal tissue can exploit the cone-beam geometry at high magnification M using a nanofocus transmission x-ray tube (nanotube) with a 300 nm minimal spot size (Excillum), combined with a single-photon counting camera. Tightly approaching the source spot with the biopsy punch, we achieve high M≈101−102, high flux density, and exploit the superior efficiency of this detector technology. Approach: Different nanotube configurations such as spot size and flux, M, as well as exposure time, Fresnel number, and coherence are varied and selected in view of resolution, field of view, and/or phase-contrast requirements. Results: The data show that the information content for the cytoarchitecture is enhanced by the phase effect. Comparison of results to those obtained at a microfocus rotating-anode x-ray tomography setup with a high-resolution detector, i.e., in low-M geometry, reveals similar to slightly superior data quality for the nanotube setup. In addition to its compactness, reduced power consumption by a factor of 103, and shorter scan duration, the particular advantage of the nanotube setup also lies in its suitability for pixel detector technology, enabling an increased range of opportunities for applications in laboratory phase-contrast x-ray tomography. Conclusions: The phase retrieval scheme utilized mixes amplitude and phase contrast, with results being robust with respect to reconstruction parameters. Structural information content is comparable to slightly superior to previous results achieved with a microfocus rotating-anode setup but can be obtained in shorter scan time. Beyond advantages as compactness, lowered power consumption, and flexibility, the nanotube setup’s scalability in view of the progress in pixel detector technology is particularly beneficial. Further progress is thus likely to bring 3-D virtual histology to the performance in scan time and throughput required for clinical practice in neuropathology.
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Affiliation(s)
- Marina Eckermann
- University of Göttingen, Institute for X-Ray Physics, Göttingen, Germany.,University of Göttingen, Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells", Göttingen, Germany
| | - Mareike Töpperwien
- University of Göttingen, Institute for X-Ray Physics, Göttingen, Germany
| | - Anna-Lena Robisch
- University of Göttingen, Institute for X-Ray Physics, Göttingen, Germany
| | | | - Christine Stadelmann
- University Medical Center Göttingen, Institute for Neuropathology, Göttingen, Germany
| | - Tim Salditt
- University of Göttingen, Institute for X-Ray Physics, Göttingen, Germany.,University of Göttingen, Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells", Göttingen, Germany
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24
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Robisch AL, Eckermann M, Töpperwien M, van der Meer F, Stadelmann C, Salditt T. Nanoscale x-ray holotomography of human brain tissue with phase retrieval based on multienergy recordings. J Med Imaging (Bellingham) 2020; 7:013501. [PMID: 32016134 PMCID: PMC6975131 DOI: 10.1117/1.jmi.7.1.013501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/24/2019] [Indexed: 11/14/2022] Open
Abstract
X-ray cone-beam holotomography of unstained tissue from the human central nervous system reveals details down to subcellular length scales. This visualization of variations in the electron density of the sample is based on phase-contrast techniques using intensities formed by self-interference of the beam between object and detector. Phase retrieval inverts diffraction and overcomes the phase problem by constraints such as several measurements at different Fresnel numbers for a single projection. Therefore, the object-to-detector distance (defocus) can be varied. However, for cone-beam geometry, changing defocus changes magnification, which can be problematic in view of image processing and resolution. Alternatively, the photon energy can be altered (multi-E). Far from absorption edges, multi-E data yield the wavelength-independent electron density. We present the multi-E holotomography at the Göttingen Instrument for Nano-Imaging with X-Rays (GINIX) setup of the P10 beamline at Deutsches Elektronen-Synchrotron. The instrument is based on a combined optics of elliptical mirrors and an x-ray waveguide positioned in the focal plane for further coherence, spatial filtering, and high numerical aperture. Previous results showed the suitability of this instrument for nanoscale tomography of unstained brain tissue. We demonstrate that upon energy variation, the focal spot is stable enough for imaging. To this end, a double-crystal monochromator and automated alignment routines are required. Three tomograms of human brain tissue were recorded and jointly analyzed using phase retrieval based on the contrast transfer function formalism generalized to multiple photon energies. Variations of the electron density of the sample are successfully reconstructed.
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Affiliation(s)
- Anna-Lena Robisch
- Georg-August-Universität Göttingen, Institut für Röntgenphysik, Göttingen, Germany
| | - Marina Eckermann
- Georg-August-Universität Göttingen, Institut für Röntgenphysik, Göttingen, Germany.,University of Göttingen, Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells," Göttingen, Germany
| | - Mareike Töpperwien
- Georg-August-Universität Göttingen, Institut für Röntgenphysik, Göttingen, Germany
| | - Franziska van der Meer
- Universitätsmedizin Göttingen, Institut für Neuropathologie, Klinik für Neurologie, Göttingen, Germany
| | - Christine Stadelmann
- Universitätsmedizin Göttingen, Institut für Neuropathologie, Klinik für Neurologie, Göttingen, Germany
| | - Tim Salditt
- Georg-August-Universität Göttingen, Institut für Röntgenphysik, Göttingen, Germany.,University of Göttingen, Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells," Göttingen, Germany
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25
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Kunishima N, Takeda Y, Hirose R, Kalasová D, Šalplachta J, Omote K. Visualization of internal 3D structure of small live seed on germination by laboratory-based X-ray microscopy with phase contrast computed tomography. PLANT METHODS 2020; 16:7. [PMID: 32021643 PMCID: PMC6995115 DOI: 10.1186/s13007-020-0557-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 01/22/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND The visualization of internal 3D-structure of tissues at micron resolutions without staining by contrast reagents is desirable in plant researches, and it can be achieved by an X-ray computed tomography (CT) with a phase-retrieval technique. Recently, a laboratory-based X-ray microscope adopting the phase contrast CT was developed as a powerful tool for the observation of weakly absorbing biological samples. Here we report the observation of unstained pansy seeds using the laboratory-based X-ray phase-contrast CT. RESULTS A live pansy seed within 2 mm in size was simply mounted inside a plastic tube and irradiated by in-house X-rays to collect projection images using a laboratory-based X-ray microscope. The phase-retrieval technique was applied to enhance contrasts in the projection images. In addition to a dry seed, wet seeds on germination with the poorer contrasts were tried. The phase-retrieved tomograms from both the dry and the wet seeds revealed a cellular level of spatial resolutions that were enough to resolve cells in the seeds, and provided enough contrasts to delineate the boundary of embryos manually. The manual segmentation allowed a 3D rendering of embryos at three different stages in the germination, which visualized an overall morphological change of the embryo upon germination as well as a spatial arrangement of cells inside the embryo. CONCLUSIONS Our results confirmed an availability of the laboratory-based X-ray phase-contrast CT for a 3D-structural study on the development of small seeds. The present method may provide a unique way to observe live plant tissues at micron resolutions without structural perturbations due to the sample preparation.
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Affiliation(s)
- Naoki Kunishima
- X-Ray Research Laboratory, Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima, Tokyo, 196-8666 Japan
| | - Yoshihiro Takeda
- X-Ray Research Laboratory, Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima, Tokyo, 196-8666 Japan
| | - Raita Hirose
- X-Ray Research Laboratory, Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima, Tokyo, 196-8666 Japan
| | - Dominika Kalasová
- CEITEC-Central European Institute of Technology, Brno University of Technology, Purkynova 123, 612 00 Brno, Czech Republic
| | - Jakub Šalplachta
- CEITEC-Central European Institute of Technology, Brno University of Technology, Purkynova 123, 612 00 Brno, Czech Republic
| | - Kazuhiko Omote
- X-Ray Research Laboratory, Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima, Tokyo, 196-8666 Japan
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