Microscopy Reference Life-Sciences
Microscopy Reference Life-Sciences
X-ray computed tomography (X-ray CT) describes the acquisition and reconstruction of 2D X-ray
transmission images to create a 3D representation of the specimen. Along with the increasing availability
of suitable staining and mounting protocols, the use of X-ray CT in life science research is rapidly
growing. The key benefit of imaging with X-rays is that it can be done without physically sectioning the
specimen. For life scientists who study physiological structures, this can be extremely valuable.
While fluorescence microscopy is used to visualize specific, labelled structures and electron microscopy
(EM) offers ultraresolution information of smaller regions of interest, X-ray CT offers larger volumes
of structural information. Additionally, X-ray CT can streamline electron microscopy and synchrotron
workflows by quickly acquiring a 3D overview dataset to check sample quality and guide subsequent,
higher resolution acquisitions.
Figure 1 The Xradia Versa architecture uses a two-stage magnification technique (geometric plus optical) for the unique capability to provide submicron resolution
at large working distances. This is known as resolution at a distance (RaaD) and makes Xradia Versa a flexible solution for a large range of sample types and sizes.
2
ZEISS Xradia Versa in Life Science Research Y. Zhang et al. (2022) Sample Preparation and Warping
The ZEISS Xradia Versa family of X-ray microscopes provides high Accuracy for Correlative Multimodal Imaging in the
contrast, high resolution 3D imaging of delicate biological sam- Mouse Olfactory Bulb Using 2-Photon, Synchrotron
ples including mineralized and soft tissues, individual organs and X-Ray and Volume Electron Microscopy. Frontiers in Cell
organoids, embryos and whole animals, insects, fossils, plant and Developmental Biology 10: 2296-634,
tissues and more. The ability to study internal histology and https://doi.org/10.3389/fcell.2022.880696
structure, even down to a cellular level, without destroying the
sample with dissection, is driving new discoveries and is gaining Y. Lu et al. (2021) Large-scale 3D imaging of mouse
traction across many different life science research fields. cochlea using serial block-face scanning electron micros-
The following pages provide a sample of peer reviewed publi- copy. STAR Protocols, Volume 2, Issue 2, 100515,
cations in biological research that have benefitted from using https://doi.org/10.1016/j.xpro.2021.100515
the ZEISS Xradia Versa XRM for high resolution and contrast
3D imaging. These publications illustrate not only how X-ray L. A. Scott et al. (2021) Characterisation of microvessel
microscopy is enabling new scientific insights across diverse blood velocity and segment length in the brain using
research fields but also how ZEISS Xradia Versa is compatible multi-diffusion-time diffusion-weighted MRI. J Cereb
with a wide range of specimen types. Blood Flow Metab. 41(8):1939-1953,
https://doi.org/10.1177/0271678X20978523
Neuroscience
From understanding our basic biology and body function to M. G. Haberl et al. (2018) CDeep3M—Plug-and-Play
developing therapeutics for disease, aging or injuries that impact cloud-based deep learning for image segmentation. Nat
the brain or nervous system, neuroscience is a thriving field of Methods 15, 677–680,
research. Establishing the relationship between structure and https://doi.org/10.1038/s41592-018-0106-z
function of neurons and brain tissue and how these relate to
behaviour and wellbeing is a formidable challenge that demands T. Katchalski et al. (2018) Iron-specific Signal Separation
a multidisciplinary approach. Multiscale analysis of structure is from within Heavy Metal Stained Biological Samples
an important part of this understanding and X-ray microscopy Using X-Ray Microtomography with Polychromatic
delivers the high-resolution, non-destructive capability to Source and Energy-Integrating Detectors. Sci Rep 8, 7553,
provide vital insights. Some neuroscience discoveries found https://doi.org/10.1038/s41598-018-25099-z
using high resolution X-ray imaging with ZEISS Xradia Versa are
provided below. J. P. Choi et al. (2016) Micro-CT Imaging Reveals Mekk3
Heterozygosity Prevents Cerebral Cavernous Malforma-
C. Bosch et al. (2022) Functional and multiscale 3D struc- tions in Ccm2-Deficient Mice. PLoS ONE 11(8): e0160833,
tural investigation of brain tissue through correlative https://doi.org/10.1371/journal.pone.0160833
in vivo physiology, synchrotron microtomography and
volume electron microscopy. Nat. Commun. 13: 2923, J. Ng et al. (2016) Genetically targeted 3D visualisation
https://doi.org/10.1038/s41467-022-30199-6 of Drosophila neurons under Electron Microscopy and
X-Ray Microscopy using miniSOG. Sci Rep 6, 38863,
K. Song et al. (2022) High-contrast en-bloc staining of https://doi.org/10.1038/srep38863
mouse whole-brain samples for EM-based connectomics.
bioRxiv 2022.03.30.486341, E. Bushong et al. (2015) X-Ray Microscopy as an Approach
https://doi.org/10.1101/2022.03.30.486341 to Increasing Accuracy and Efficiency of Serial Block-Face
Imaging for Correlated Light and Electron Microscopy of
S. Ströh et al. (2022) In situ X-ray assisted electron Biological Specimens. Microscopy and Microanalysis, 21(1),
microscopy staining for large biological samples. 231-238,
eLife 11: e72147, https://doi.org/10.1017/s1431927614013579
https://doi.org/10.7554/eLife.72147
3
Soft Tissue
From 3D cultures and tumors to entire organs or developing C. Hsu et al. (2019) High resolution imaging of mouse
embryos, researchers have been interested in visualization the embryos and neonates with X-ray micro-computed
internal structures of these soft tissues to find new insights in tomography. Current Protocols in Mouse Biology, 9: e63,
cancer research, vascular research, developmental biology, tissue https://doi.org/10.1002/cpmo.63
engineering, histology and more. Some examples of non-de-
structive, high-resolution imaging of soft tissues using ZEISS M. Busse et al. (2018) Bismuth-Oxo-Clusters for Soft-Tissue
Xradia Versa in scientific literature are provided below. Staining. Microscopy and Microanalysis, 24(S2), 366-367.
https://doi.org/10.1017/S1431927618014125
S. Matthews et al. (2021) Polystyrene micro- and nanoplas-
tics affect locomotion and daily activity of Drosophila T. Hatani et al. (2018) Nano-structural analysis of engrafted
melanogaster. Environ. Sci.: Nano, 8: 110-121, human induced pluripotent stem cell-derived cardiomy-
https://doi.org/10.1039/D0EN00942C ocytes in mouse hearts using a genetic-probe APEX2.
Biochemical and Biophysical Research Communications,
B. A. Metscher (2021) A simple nuclear contrast staining Volume 505, Issue 4, Pages 1251-1256,
method for microCT-based 3D histology using lead(II) https://doi.org/10.1016/j.bbrc.2018.10.020
acetate. J. Anat. 238: 1036– 1041,
https://doi.org/10.1111/joa.13351 M. Hoshi et al. (2018) Reciprocal Spatiotemporally Con-
trolled Apoptosis Regulates Wolffian Duct Cloaca Fusion.
Y. Sergey et al. (2021) Visualization of different anatomical J Am Soc Nephrol. 29(3):775-783,
parts of the enucleated human eye using X-ray micro-CT https://doi.org/10.1681/ASN.2017040380
imaging. Experimental Eye Research, Volume 203: 108394,
https://doi.org/10.1016/j.exer.2020.108394 Bone and Mineralized Tissue
Understanding the structure and mechanical properties of
Y. Yu et al. (2021) Close to Real: Large-Volume 3D Cell mineralized tissue, like bone and cartilage, as well as associ-
Spheroids on a Superamphiphobic Surface. Adv. Mater. ated muscles and tendons is a thriving area of research with
Interfaces 2021, 8, 2100039. exciting developments in foundational understanding as well as
https://doi.org/10.1002/admi.202100039 therapeutic technologies. X-ray imaging is invaluable in skeletal
research for capturing a wide range of bone morphometry mea-
Q. Chu et al. (2020) CACCT: An Automated Tool of surements both in vivo and in dissected specimens. Additional
Detecting Complicated Cardiac Malformations in Mouse insights into the micro- and nano-structure of bone at higher
Models. Adv. Sci. 7, 1903592, resolution are pivotal to determine bone quality and mechanical
https://doi.org/10.1002/advs.201903592 properties and this is where X-ray microscopy is extremely valu-
able. Some recent examples of the latest possibilities in skeletal
N. Eder et al. (2020) YAP1/TAZ drives ependymoma-like biology using high resolution X-ray microscopy with ZEISS Xradia
tumour formation in mice. Nat Commun 11, 2380, Versa are provided below.
https://doi.org/10.1038/s41467-020-16167-y
A. Karali et al. (2022) Full-field strain of regenerated bone
J. Marcé-Nogué et al. (2020) Evaluating fidelity of CT based tissue in a femoral fracture model. Journal of Microscopy,
3D models for Zebrafish conductive hearing system. 285: 156-166,
Micron, Volume 135, 102874, https://doi.org/10.1111/jmi.12937
https://doi.org/10.1016/j.micron.2020.102874
M. S. White et al. (2022) Relationship between altered
N. Yoshida et al. (2020) The zebrafish as a novel model for knee kinematics and subchondral bone remodeling in
the in vivo study of Toxoplasma gondii replication and a clinically translational model of ACL injury. Journal of
interaction with macrophages. Dis Model Mech 13 (7), Orthopaedic Research, Volume 40 (1): 74-86,
https://doi.org/10.1242/dmm.043091 https://doi.org/10.1002/jor.24943
P. Bidola et al. (2019) A step towards valid detection and N. K. Wittig et al. (2022) Opportunities for biomineraliza-
quantification of lung cancer volume in experimental tion research using multiscale computed X-ray tomogra-
mice with contrast agent-based X-ray microtomography. phy as exemplified by bone imaging. Journal of Structural
Sci Rep 9, 1325, Biology, Volume 214, Issue 1, 107822,
https://doi.org/10.1038/s41598-018-37394-w https://doi.org/10.1016/j.jsb.2021.107822
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R. Bonithon et al. (2021) Multi-scale mechanical and F. Lacoviello et al. (2020) The multiscale hierarchical
morphological characterisation of sintered porous structure of Heloderma suspectum osteoderms and their
magnesium-based scaffolds for bone regeneration in mechanical properties. Acta Biomaterialia, Volume 107:
critical-sized defects. Acta Biomaterialia 127; 338-352, 194-203,
https://doi.org/10.1016/j.actbio.2021.03.068 https://doi.org/10.1016/j.actbio.2020.02.029
R. S. Chisena et al. (2021) Novel preclinical method for N. Reznikov et al. (2020) Deep learning for 3D imaging and
evaluating the efficacy of a percutaneous treatment in image analysis in biomineralization research. Journal of
human ex vivo calcified plaque. Med. Biol. Eng. Comput. Structural Biology, Volume 212 (1): 107598,
59: 799–811, https://doi.org/10.1016/j.jsb.2020.107598
https://doi.org/10.1007/s11517-021-02334-w
G. Tozzi et al. (2020) Full-Field Strain Uncertainties and
I. Dumbryte et al. (2021) Three-dimensional non-destructive Residuals at the Cartilage-Bone Interface in Unstained
visualization of teeth enamel microcracks using X-ray Tissues Using Propagation-Based Phase-Contrast XCT
micro-computed tomography. Sci. Rep. 11: 14810, and Digital Volume Correlation. Materials, 13, 2579,
https://doi.org/10.1038/s41598-021-94303-4 https://doi.org/10.3390/ma13112579
A. Karali et al. (2021) Micromechanical evaluation of A. Grüneboom et al. (2019) A network of trans-cortical
cortical bone using in situ XCT indentation and digital capillaries as mainstay for blood circulation in long
volume correlation. Journal of the Mechanical Behavior of bones. Nat. Metab. 1: 236–250,
Biomedical Materials, Volume 115; 104298, https://doi.org/10.1038/s42255-018-0016-5
https://doi.org/10.1016/j.jmbbm.2020.104298
M. Peña Fernández et al. (2019) Full-Field Strain Analysis of
J. Sartori and H. Stark (2021) Tracking tendon fibers to their Bone–Biomaterial Systems Produced by the Implantation
insertion – a 3D analysis of the Achilles tendon enthesis of Osteoregenerative Biomaterials in an Ovine Model.
in mice. Acta Biomaterialia, Volume 120: 146-155, ACS Biomater. Sci. Eng. 5 (5): 2543–2554,
https://doi.org/10.1016/j.actbio.2020.05.001 https://doi.org/10.1021/acsbiomaterials.8b01044
D. Buss et al. (2020) Crossfibrillar mineral tessellation in N. Reznikov et al. (2019) Individual response variations in
normal and Hyp mouse bone as revealed by 3D FIB-SEM scaffold-guided bone regeneration are determined by
microscopy. Journal of Structural Biology, Volume 212 (2): independent strain- and injury-induced mechanisms.
107603, Biomaterials, Volume 194, Pages 183-194,
https://doi.org/10.1016/j.jsb.2020.107603 https://doi.org/10.1016/j.biomaterials.2018.11.026
R. K. Dirkes et al. (2020) Global estrogen receptor-α knock- I. A. Fiedler et al. (2018) Severely Impaired Bone Material
out has differential effects on cortical and cancellous Quality in Chihuahua Zebrafish Resembles Classical
bone in aged male mice. FACETS, 5(1): 328-348, Dominant Human Osteogenesis Imperfecta. J. Bone Miner.
https://doi.org/10.1139/facets-2019-0043 Res. 33:1489-1499,
https://doi.org/10.1002/jbmr.3445
H. Haimov et al. (2020) Mineralization pathways in the
active murine epiphyseal growth plate. Bone, Volume 130:
115086,
https://doi.org/10.1016/j.bone.2019.115086
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Plant Science K. Chen et al. (2019) NAL8 encodes a prohibitin that con-
As the world population grows, the need for sustainable and tributes to leaf and spikelet development by regulating
more nutritious sources of food becomes increasingly important. mitochondria and chloroplasts stability in rice. BMC Plant
Some plant researchers have been working to understand how Biol. 19: 395,
external influences can impact crop and the crop yield. Using https://doi.org/10.1186/s12870-019-2007-4
X-ray imaging to reach cellular level understandings in the whole
plant without having to trim the sample down into smaller A. Dirks-Mulder et al. (2019) Morphological and Molecular
pieces is revolutionary since these insights are unreachable Characterization of Orchid Fruit Development. Frontiers in
through other means. All parts of the plant from structures Plant Science, Volume 10: Article 137,
such as seeds to inflorescence, leaves and shoots to visualizing https://doi.org/10.3389/fpls.2019.00137
undisturbed plant roots and their mycorrhizal relationships is
all extremely valuable to researchers. The growing use of high K. Duncan et al. (2019) Using 3D X-ray Microscopy to Study
resolution X-ray microscopy with ZEISS Xradia Versa in plant Crown Root Development and Primary Root Tip Growth
science is nicely represented in the below publications: in Diverse Maize (Zea mays L.) Lines. Microscopy and
Microanalysis, 25(S2): 1032-1033,
K. L. Cox Jr et al. (2022) Organizing your space: The https://doi.org/10.1017/S1431927619005890
potential for integrating spatial transcriptomics and 3D
imaging data in plants. Plant Physiology, Volume 188 (2): Natural history
703–712, Scientists working in natural history are interested in both
https://doi.org/10.1093/plphys/kiab508 discovering new insights from ancient specimens as well as con-
serving them for future generations. However, in many cases the
K. E. Duncan et al. (2022) X-ray microscopy enables multi- specimens of interest are extremely precious, often unique, and
scale high-resolution 3D imaging of plant cells, tissues, need to be treated with the utmost care. Non-destructive X-ray
and organs. Plant Physiology, Volume 188, Issue 2, Pages imaging is therefore hugely valuable for capturing the internal
831–845, structure of these precious specimens without damage. The
https://doi.org/10.1093/plphys/kiab405 high-resolution 3D insights that can be reached using the Xradia
Versa XRM provide levels of detail that continue to support
K. Chen et al. (2021) Microstructure investigation of plant exciting finds in the natural history realm. Some examples that
architecture with X-ray microscopy. Plant Science, Volume leverage ZEISS Xradia Versa can be found in the publications
311, 110986, that follow.
https://doi.org/10.1016/j.plantsci.2021.110986
A. Casadei-Ferreira et al. (2021) Head and mandible shapes
B. Han et al. (2021) Gaseous environment modulates are highly integrated yet represent two distinct modules
volatile emission and viability loss during seed artificial within and among worker subcastes of the ant genus
ageing. Planta, 253: 106, Pheidole. Ecology and Evolution, Volume 11 (11): 6104-6118,
https://doi.org/10.1007/s00425-021-03620-5 https://doi.org/10.1002/ece3.7422
P. Mehra et al. (2021) Changes in soil-pores and wheat root M. J. R. Hall et al. (2021) Micro-CT imaging of Onchocerca
geometry due to strategic tillage in a no-tillage cropping infection of Simulium damnosum s.l. blackflies and
system. Soil Research, 59: 83-96, comparison of the peritrophic membrane thickness of
https://doi.org/10.1071/SR20010 forest and savannah flies. Med. Vet. Entomol. 35: 231-238,
https://doi.org/10.1111/mve.12509
T. Guo et al. (2020) A SAC Phosphoinositide Phosphatase
Controls Rice Development via Hydrolyzing PI4P and A. Jochuma et al. (2021) Mother snail labors for posterity
PI(4,5)P2. Plant Physiol. 182(3): 1346-1358, in bed of mid-Cretaceous amber. Gondwana Research,
https://doi.org/10.1104/pp.19.01131 Volume 97: 68-72,
https://doi.org/10.1016/j.gr.2021.05.006
A. Heiduk et al. (2020) Pitfall Flower Development and
Organ Identity of Ceropegia sandersonii (Apocynace-
ae-Asclepiadoideae). Plants, 9: 1767,
https://doi.org/10.3390/plants9121767
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S. Koch et al. (2021) Nano-CT imaging of larvae in the ant Directed Multimodal Workflows
Pheidole hyatti reveals coordinated growth of a rudi- Sample investigation often benefits from using more than one
mentary organ necessary for soldier development. J Exp imaging approach since the combined information can provide
Zool B (Mol Dev Evol), 336: 540– 553, greater value than the sum of the individual datasets. Such
https://doi.org/10.1002/jez.b.23097 multimodal imaging approaches are increasingly used for many
different specimen types and application areas. X-ray imaging
R. Kundrata et al. (2021) A new enigmatic lineage of can be a critical tool in such multimodal workflows by providing
Dascillidae (Coleoptera: Elateriformia) from Eocene Baltic a bridge between functional data from light microscopy and
amber described using X-ray microtomography, with ultrastructural insights from electron microscopy or synchrotron
notes on Karumiinae morphology and classification. Foss. data. The high resolution and contrast imaging provided by
Rec, 24: 141–149, the Xradia Versa XRM supports selection of the most optimal
https://doi.org/10.5194/fr-24-141-2021 specimens and precise localization of the region of interest for
high acquisition imaging. Some examples of the use of high
J. Wang et al. (2021) A monotreme-like auditory apparatus resolution 3D X-ray microscopy with ZEISS Xradia Versa as part
in a Middle Jurassic haramiyidan. Nature, 590: 279–283, of a multimodal imaging workflow are provided below.
https://doi.org/10.1038/s41586-020-03137-z
S. Agarwala et al. (2022) Defining the ultrastructure of the
R. Kundrata et al. (2020) X-ray micro-computed tomogra- hematopoietic stem cell niche by correlative light and
phy reveals a unique morphology in a new click-beetle electron microscopy. eLife 11: e64835,
(Coleoptera, Elateridae) from the Eocene Baltic amber. https://doi.org/10.7554/eLife.64835
Sci. Rep. 10: 20158,
https://doi.org/10.1038/s41598-020-76908-3 C. Bosch et al. (2022) Functional and multiscale 3D struc-
tural investigation of brain tissue through correlative
C. Peeters et al. (2020) The loss of flight in ant workers in vivo physiology, synchrotron microtomography and
enabled an evolutionary redesign of the thorax for volume electron microscopy. Nat. Commun. 13: 2923,
ground labour. Front. Zool. 17: 33, https://doi.org/10.1038/s41467-022-30199-6
https://doi.org/10.1186/s12983-020-00375-9
Y. Zhang et al. (2022) Sample Preparation and Warping
H. Wang et al. (2020) Exceptional preservation of repro- Accuracy for Correlative Multimodal Imaging in the
ductive organs and giant sperm in Cretaceous ostracods. Mouse Olfactory Bulb Using 2-Photon, Synchrotron
Proceedings of the Royal Society B: Biological Sciences, X-Ray and Volume Electron Microscopy. Frontiers in Cell
Volume 287 (1935), and Developmental Biology 10: 2296-634
https://doi.org/10.1098/rspb.2020.1661 https://doi.org/10.3389/fcell.2022.880696
M. Doeland et al. (2019) Tooth replacement in early sarcop- Y. Lu et al. (2021) Large-scale 3D imaging of mouse
terygians. Royal Society Open Science. Volume 6: Issue 11, cochlea using serial block-face scanning electron micros-
https://doi.org/10.1098/rsos.191173 copy. STAR Protocols, Volume 2, Issue 2, 100515,
https://doi.org/10.1016/j.xpro.2021.100515
Z. Johanson et al. (2019) The Synarcual of the Little Skate,
Leucoraja erinacea: Novel Development Among the A. A. Polilov et al. (2021) Protocol for preparation of
Vertebrates. Front. Ecol. Evol, vol 7: article 12, heterogeneous biological samples for 3D electron
https://doi.org/10.3389/fevo.2019.00012 microscopy: a case study for insects. Sci Rep 11: 4717,
https://doi.org/10.1038/s41598-021-83936-0
D. Martín-Vega et al. (2018) 3D virtual histology at the
host/parasite interface: visualisation of the master A. V. Weigel et al. (2021) ER-to-Golgi protein delivery
manipulator, Dicrocoelium dendriticum, in the brain of through an interwoven, tubular network extending from
its ant host. Sci Rep 8, 8587, ER. Cell 184 (9): 2412-2429.e16,
https://doi.org/10.1038/s41598-018-26977-2 https://doi.org/10.1016/j.cell.2021.03.035
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P. O. Bayguinov et al. (2020) Assaying three-dimensional
cellular architecture using X-ray tomographic and
correlated imaging approaches. J. Biol. Chem. 295(46):
15782–15793,
https://doi.org/10.1074/jbc.REV120.009633
8
Cover images:
Rat Heart: Courtesy of University of Radboud, Netherlands.
Pig eye: Data courtesy of Prof. Rachel Williams, Dr. Brendan Geraghty,
Dr. Victoria Kearns, Valentin Pied and Dr. Julia Behnsen,
University of Liverpool, UK.
Mouse bone: Sample from the collection of Daniel Wescott, University of
Not for therapeutic use, treatment or medical diagnostic evidence. Not all products are available in every country. Contact your local ZEISS representative for more information.
Texas at San Marcos. Imagery and analysis performed using
Dragonfly Pro Bone Analysis module.
Mouse embryo: Sample courtesy of Massachusetts General Hospital.
Zebrafish: Animation from Suniaga, S., Rolvien, T., vom Scheidt, A. et al.
Increased mechanical loading through controlled swimming
exercise induces bone formation and mineralization in adult
zebrafish. Sci Rep 8, 3646 (2018).
EN_41_013_289 | CZ 12-2022 | Design, scope of delivery and technical progress subject to change without notice. | © Carl Zeiss Microscopy GmbH