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Scherberich J, Windfelder AG, Krombach GA. Analysis of fixation materials in micro-CT: It doesn't always have to be styrofoam. PLoS One 2023; 18:e0286039. [PMID: 37315002 DOI: 10.1371/journal.pone.0286039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/08/2023] [Indexed: 06/16/2023] Open
Abstract
Good fixation of filigree specimens for micro-CT examinations is often a challenge. Movement artefacts, over-radiation or even crushing of the specimen can easily occur. Since different specimens have different requirements, we scanned, analysed and compared 19 possible fixation materials under the same conditions in the micro-CT. We focused on radiodensity, porosity and reversibility of these fixation materials. Furthermore, we have made sure that all materials are cheap and easily available. The scans were performed with a SkyScan 1173 micro-CT. All dry fixation materials tested were punched into 5 mm diameter cylinders and clamped into 0.2 ml reaction vessels. A voxel size of 5.33 μm was achieved in a 180° scan in 0.3° steps. Ideally, fixation materials should not be visible in the reconstructed image, i.e., barely binarised. Besides common micro-CT fixation materials such as styrofoam (-935 Hounsfield Units) or Basotect foam (-943 Hounsfield Units), polyethylene air cushions (-944 Hounsfield Units), Micropor foam (-926 Hounsfield Units) and polyurethane foam, (-960 Hounsfield Units to -470 Hounsfield Units) have proved to be attractive alternatives. Furthermore, more radiopaque materials such as paraffin wax granulate (-640 Hounsfield Units) and epoxy resin (-190 Hounsfield Units) are also suitable as fixation materials. These materials often can be removed in the reconstructed image by segmentation. Sample fixations in the studies of recent years are almost all limited to fixation in Parafilm, Styrofoam, or Basotect foam if the fixation type is mentioned at all. However, these are not always useful, as styrofoam, for example, dissolves in some common media such as methylsalicylate. We show that micro-CT laboratories should be equipped with various fixation materials to achieve high-level image quality.
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Affiliation(s)
- Jan Scherberich
- Department of Diagnostic and Interventional Radiology (Experimental Radiology), University Hospital Giessen, Giessen, Hesse, Germany
| | - Anton G Windfelder
- Department of Diagnostic and Interventional Radiology (Experimental Radiology), University Hospital Giessen, Giessen, Hesse, Germany
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Giessen, Hesse, Germany
| | - Gabriele A Krombach
- Department of Diagnostic and Interventional Radiology (Experimental Radiology), University Hospital Giessen, Giessen, Hesse, Germany
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Kolmann MA, Nagesan RS, Andrews JV, Borstein SR, Figueroa RT, Singer RA, Friedman M, López-Fernández H. DiceCT for fishes: recommendations for pairing iodine contrast agents with μCT to visualize soft tissues in fishes. JOURNAL OF FISH BIOLOGY 2023; 102:893-903. [PMID: 36647819 DOI: 10.1111/jfb.15320] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 01/11/2023] [Indexed: 06/17/2023]
Abstract
Computed tomography (CT) scanning and other high-throughput three-dimensional (3D) visualization tools are transforming the ways we study morphology, ecology and evolutionary biology research beyond generating vast digital repositories of anatomical data. Contrast-enhanced chemical staining methods, which render soft tissues radio-opaque when coupled with CT scanning, encompass several approaches that are growing in popularity and versatility. Of these, the various diceCT techniques that use an iodine-based solution like Lugol's have provided access to an array of morphological data sets spanning extant vertebrate lineages. This contribution outlines straightforward means for applying diceCT techniques to preserved museum specimens of cartilaginous and bony fishes, collectively representing half of vertebrate species diversity. This study contrasts the benefits of using either aqueous or ethylic Lugol's solutions and reports few differences between these methods with respect to the time required to achieve optimal tissue contrast. It also explores differences in minimum stain duration required for different body sizes and shapes and provides recommendations for staining specimens individually or in small batches. As reported by earlier studies, the authors note a decrease in pH during staining with either aqueous or ethylic Lugol's. Nonetheless, they could not replicate the drastic declines in pH reported elsewhere. They provide recommendations for researchers and collections staff on how to incorporate diceCT into existing curatorial practices, while offsetting risk to specimens. Finally, they outline how diceCT with Lugol's can aid ichthyologists of all kinds in visualizing anatomical structures of interest: from brains and gizzards to gas bladders and pharyngeal jaw muscles.
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Affiliation(s)
- Matthew A Kolmann
- University of Michigan Museum of Paleontology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Biology, University of Louisville, Louisville, Kentucky, USA
| | - Ramon S Nagesan
- Department of Ecology & Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, Michigan, USA
| | - James V Andrews
- University of Michigan Museum of Paleontology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Samuel R Borstein
- Department of Ecology & Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, Michigan, USA
| | - Rodrigo Tinoco Figueroa
- University of Michigan Museum of Paleontology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Randal A Singer
- Department of Ecology & Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, Michigan, USA
| | - Matt Friedman
- University of Michigan Museum of Paleontology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Hernán López-Fernández
- Department of Ecology & Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, Michigan, USA
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Castilla-Ibeas A, Zdral S, Galán L, Haro E, Allou L, Campa VM, Icardo JM, Mundlos S, Oberg KC, Ros MA. Failure of digit tip regeneration in the absence of Lmx1b suggests Lmx1b functions disparate from dorsoventral polarity. Cell Rep 2023; 42:111975. [PMID: 36641754 DOI: 10.1016/j.celrep.2022.111975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 11/07/2022] [Accepted: 12/22/2022] [Indexed: 01/15/2023] Open
Abstract
Mammalian digit tip regeneration is linked to the presence of nail tissue, but a nail-explicit model is missing. Here, we report that nail-less double-ventral digits of ΔLARM1/2 mutants that lack limb-specific Lmx1b enhancers fail to regenerate. To separate the nail's effect from the lack of dorsoventral (DV) polarity, we also interrogate double-dorsal double-nail digits and show that they regenerate. Thus, DV polarity is not a prerequisite for regeneration, and the nail requirement is supported. Transcriptomic comparison between wild-type and non-regenerative ΔLARM1/2 mutant blastemas reveals differential upregulation of vascularization and connective tissue functional signatures in wild type versus upregulation of inflammation in the mutant. These results, together with the finding of Lmx1b expression in the postnatal dorsal dermis underneath the nail and uniformly in the regenerative blastema, open the possibility of additional Lmx1b roles in digit tip regeneration, in addition to the indirect effect of mediating the formation of the nail.
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Affiliation(s)
- Alejandro Castilla-Ibeas
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC; CSIC-SODERCAN-UC), Santander, Spain
| | - Sofía Zdral
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC; CSIC-SODERCAN-UC), Santander, Spain
| | - Laura Galán
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC; CSIC-SODERCAN-UC), Santander, Spain
| | - Endika Haro
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC; CSIC-SODERCAN-UC), Santander, Spain
| | - Lila Allou
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Víctor M Campa
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC; CSIC-SODERCAN-UC), Santander, Spain
| | - Jose M Icardo
- Departamento de Anatomía y Biología Celular, Universidad de Cantabria, Santander, Spain
| | - Stefan Mundlos
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Kerby C Oberg
- Department of Pathology and Human Anatomy, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Marian A Ros
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC; CSIC-SODERCAN-UC), Santander, Spain.
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Jonsson T. Micro-CT and deep learning: Modern techniques and applications in insect morphology and neuroscience. FRONTIERS IN INSECT SCIENCE 2023; 3:1016277. [PMID: 38469492 PMCID: PMC10926430 DOI: 10.3389/finsc.2023.1016277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 01/06/2023] [Indexed: 03/13/2024]
Abstract
Advances in modern imaging and computer technologies have led to a steady rise in the use of micro-computed tomography (µCT) in many biological areas. In zoological research, this fast and non-destructive method for producing high-resolution, two- and three-dimensional images is increasingly being used for the functional analysis of the external and internal anatomy of animals. µCT is hereby no longer limited to the analysis of specific biological tissues in a medical or preclinical context but can be combined with a variety of contrast agents to study form and function of all kinds of tissues and species, from mammals and reptiles to fish and microscopic invertebrates. Concurrently, advances in the field of artificial intelligence, especially in deep learning, have revolutionised computer vision and facilitated the automatic, fast and ever more accurate analysis of two- and three-dimensional image datasets. Here, I want to give a brief overview of both micro-computed tomography and deep learning and present their recent applications, especially within the field of insect science. Furthermore, the combination of both approaches to investigate neural tissues and the resulting potential for the analysis of insect sensory systems, from receptor structures via neuronal pathways to the brain, are discussed.
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Affiliation(s)
- Thorin Jonsson
- Institute of Biology, Karl-Franzens-University Graz, Graz, Austria
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Chavez MB, Chu EY, Kram V, de Castro LF, Somerman MJ, Foster BL. Guidelines for Micro-Computed Tomography Analysis of Rodent Dentoalveolar Tissues. JBMR Plus 2021; 5:e10474. [PMID: 33778330 PMCID: PMC7990153 DOI: 10.1002/jbm4.10474] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/16/2021] [Accepted: 02/09/2021] [Indexed: 12/21/2022] Open
Abstract
Micro–computed tomography (μCT) has become essential for analysis of mineralized as well as nonmineralized tissues and is therefore widely applicable in the life sciences. However, lack of standardized approaches and protocols for scanning, analyzing, and reporting data often makes it difficult to understand exactly how analyses were performed, how to interpret results, and if findings can be broadly compared with other models and studies. This problem is compounded in analysis of the dentoalveolar complex by the presence of four distinct mineralized tissues: enamel, dentin, cementum, and alveolar bone. Furthermore, these hard tissues interface with adjacent soft tissues, the dental pulp and periodontal ligament (PDL), making for a complex organ. Drawing on others' and our own experience analyzing rodent dentoalveolar tissues by μCT, we introduce techniques to successfully analyze dentoalveolar tissues with similar or disparate compositions, densities, and morphological characteristics. Our goal is to provide practical guidelines for μCT analysis of rodent dentoalveolar tissues, including approaches to optimize scan parameters (filters, voltage, voxel size, and integration time), reproducibly orient samples, define regions and volumes of interest, segment and subdivide tissues, interpret findings, and report methods and results. We include illustrative examples of analyses performed on genetically engineered mouse models with phenotypes in enamel, dentin, cementum, and alveolar bone. The recommendations are designed to increase transparency and reproducibility, promote best practices, and provide a basic framework to apply μCT analysis to the dentoalveolar complex that can also be extrapolated to a variety of other tissues of the body. © 2021 The Authors. JBMR Plus published by Wiley Periodicals LLC. on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- Michael B Chavez
- Division of Biosciences, College of Dentistry The Ohio State University Columbus OH USA
| | - Emily Y Chu
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) National Institutes of Health (NIH) Bethesda MD USA
| | - Vardit Kram
- National Institute of Dental and Craniofacial Research (NIDCR)National Institutes of Health (NIH) Bethesda MD USA
| | - Luis F de Castro
- National Institute of Dental and Craniofacial Research (NIDCR)National Institutes of Health (NIH) Bethesda MD USA
| | - Martha J Somerman
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) National Institutes of Health (NIH) Bethesda MD USA
| | - Brian L Foster
- Division of Biosciences, College of Dentistry The Ohio State University Columbus OH USA
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