#ARK #CTLabMap #DataCurationNetwork #DCN #DecemberSpecial #Discoverable #Findability #HolidayTwists #MorphoSource #ORCID #PersistentIdentifiers #ROR #RRID 3D Slicer Beginner Friendly Blender Blog Bruker Skyscan Communication and Outreach CT Basics Data Analysis Data Postprocessing Education Fiji/ImageJ Free Sample Data MeshLab Nikon OpenScience Paper PDF Phoenix GE/Waygate Physics of CT PowerPoint Reconstruction Sample Prep Scanning Segmenting VGStudio Video Website YouTube Channel Zeiss Xradia
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Micro-computed tomography for natural history specimens: a handbook of best practice protocols
Keklikoglou, Kleoniki, Sarah Faulwetter, Eva Chatzinikolaou, Patricia Wils, Jonathan Brecko, Jiří Kvaček, Brian Metscher, and Christos Arvanitidis. “Micro-computed tomography for natural history specimens: a handbook of best practice protocols.” European Journal of Taxonomy 522 (2019). https://doi.org/10.5852/ejt.2019.522
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Artefacts in X-ray microtomography of materials
Davis, G. R., and J. C. Elliott. “Artefacts in X-ray microtomography of materials.” Materials science and technology 22, no. 9 (2006): 1011-1018. https://doi.org/10.1179/174328406X114117
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diceCT: Diffusible Iodine-based Contrast-enhanced Computed Tomography
Website that has a collection of resources, blog posts, and papers relating to diceCT. Some notable papers listed on the webpage include:
Gignac, Paul M., Nathan J. Kley, Julia A. Clarke, Matthew W. Colbert, Ashley C. Morhardt, Donald Cerio, Ian N. Cost et al. “Diffusible iodine‐based contrast‐enhanced computed tomography (diceCT): an emerging tool for rapid, high‐resolution, 3‐D imaging of metazoan soft tissues.” Journal of anatomy 228, no. 6 (2016): 889-909. https://doi.org/10.1111/joa.12449
Gignac, Paul M., and Nathan J. Kley. “The utility of diceCT imaging for high-throughput comparative neuroanatomical studies.” Brain Behavior and Evolution 91, no. 3 (2018): 180-190. https://doi.org/10.1159/000485476
Orsbon, Courtney P., Nicholas J. Gidmark, and Callum F. Ross. “Dynamic musculoskeletal functional morphology: integrating diceCT and XROMM.” The Anatomical Record 301, no. 2 (2018): 378-406. https://doi.org/10.1002/ar.23714
Llambrich, Sergi, Jens Wouters, Uwe Himmelreich, Mara Dierssen, James Sharpe, Willy Gsell, Neus Martínez-Abadías, and Greetje Vande Velde. “ViceCT and whiceCT for simultaneous high-resolution visualization of craniofacial, brain and ventricular anatomy from micro-computed tomography.” Scientific Reports 10, no. 1 (2020): 18772. https://doi.org/10.1038/s41598-020-75720-3
And more!
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X-Ray Microscopy Introduction
By Jon Giencke, Bruker
X-ray Diffraction (XRD) and X-ray Microscopy (XRM) can provide a wealth of information while being non-destructive and easily accessible. This video series includes an exciting line-up of speakers to discuss the basics of the techniques, provide some real-world examples and show the techniques in action. We hope that by watching you can broaden your knowledge on how these techniques can assist in uncovering information locked inside some of the items in your collections!
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Ecology and Evolutionary Biology Museums YouTube Channel, CT Data & Segmentation Tutorial Series
By Ramon Nagesan, University of Michigan Museum of Zoology
http://University of Michigan Museum of Zoology
YouTube playlist of tutorials that range from introduction to CT Data, MorphoSource, and processing data in VGStudio.
Beginner Friendly, CT Basics, Data Analysis, Data Postprocessing, Nikon, Segmenting, VGStudio, Video
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DigiMorph
By UTCT, University of Texas
https://www.digimorph.org/index.phtml
The Digital Morphology library is a dynamic archive of information on digital morphology and high-resolution X-ray computed tomography of biological specimens.
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Spatial Archaeometry Research Collaborations (SPARC) Teaching Resources for microCT (University of Arkansas)
By Manon Wilson, University of Arkansas
https://github.com/castuofa/sparc_microct
Educational resources including CT Data analysis and visualization focused on the field of archaeology.
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3D Think Game by ERSUCC
By Isaac Brown, David Dunand, John Misiaszek, Samuel Pennell
https://ersucc.itch.io/3d-think
Test your spatial reasoning with this puzzle game inspired by tomography!
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Collections Education Coffee Break Series: oVert TCN Resources for Education
By Jaimi Gray, UTCT, University of Texas
https://qubeshub.org/publications/2760/1
A brief introduction to educational resources associated with the oVert project. This resource includes the slides and recording of Dr. Jaimi Gray’s presentation as well as links to all of the resources she discusses (doi:10.25334/95DJ-MY09)
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Gray’s Colors of Skull Anatomy
By Jaimi Gray, UTCT, University of Texas
http://www.graysvertebrateanatomy.com/work/colorsofskullanatomy/
Standardized color scheme for rendering skulls.
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University of Florida DeLeon Lab Data Post-processing Modules
By Valeria DeLeon and Rose Bryson, The University of Florida
https://www.youtube.com/@deleonlab/videos
Tutorials for analyzing and processing CT data in 3D Slicer.
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Data Processing Basics in VG Studio
By April Neander, The University of Chicago
Chapter 12 of the University of Chicago PaleoCT training course. Covers importing data, navigation, reorientation, cropping, and merging scans in VGStudio.
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3D Digital Reconstruction
By April Neander, The University of Chicago
Chapter 11 of the University of Chicago PaleoCT training course. Covers reconstruction tools available on Datos, such as AGC, cropping, and other modules.
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SlicerMorph
By SlicerMorph Team, Murat Maga, Adam Summers, and Doug Boyer
https://slicermorph.github.io/
Github page for 3D Slicer plugin that streamlines data import, visualization, measurement, annotation, and geometric morphometric analysis on 3D data, including volumetric scans (CTs and MRs) and 3D surface scans.
SlicerMorph YouTube Channel: https://www.youtube.com/channel/UCy3Uz1ikRH1B7WSMfaldcjQ
SlicerMorph Tutorials: https://github.com/SlicerMorph/Tutorials
SlicerMorph Free Sample Data: https://github.com/SlicerMorph/SampleData
3D Slicer, Data Analysis, Data Postprocessing, Free Sample Data, Reconstruction, Website, YouTube Channel
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3D Slicer Training
By 3D Slicer
https://www.slicer.org/wiki/Documentation/Nightly/Training
3D Slicer’s Wiki page of tutorials.
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MICRO Instructions for Working with Image Stacks in FIJI (FIJI Is Just ImageJ)
By Manon Wilson, Paul Gignac, and Claire Terhune from MICRO, University of Arkansas
https://micro.uark.edu/micro-instructions-for-working-with-image-stacks-in-fiji-fiji-is-just-imagej/
Tips and tricks for manipulating CT-scanner image stacks using the free software ImageJ.
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Seattle Children’s Research Institute
By Murat Maga, Seattle Children’s Research Institute
https://faculty.washington.edu/maga/SCRI_MicroCT/
Facility Website that offers CT scanning services, hosts mouse CT Data for download, 3D Visualizations, and other useful documents.
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MICRO introduction to diceCT
By Claire Terhune and Paul Gignac at MICRO, University of Arkansas
https://micro.uark.edu/introtodicect/
Tips and tricks for diceCT staining natural history specimens, which allows for the visualization of soft-tissue structure in CT scans.
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MICRO Specimen Packaging Recommendations for Optimal Mounting
By MICRO, University of Arkansas
Learn how to package your samples for optimal CT imaging.
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Reducing soft-tissue shrinkage artefacts caused by staining with Lugol’s solution
Dawood, Y., J. Hagoort, B. A. Siadari, J. M. Ruijter, Q. D. Gunst, N. H. J. Lobe, G. J. Strijkers, B. S. de Bakker, and M. J. B. van den Hoff. “Reducing soft-tissue shrinkage artefacts caused by staining with Lugol’s solution.” Scientific reports 11, no. 1 (2021): 19781. https://doi.org/10.1038/s41598-022-06160-4
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MICRO Specimen Packaging Recommendations for Optimal Mounting
From MICRO, University of Arkansas
Learn how to package your samples for optimal CT imaging.
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Additional Scan Tips
By April Neander, The University of Chicago
Chapter 9 of the University of Chicago PaleoCT training course. Covers mutliscan, observation ROI, and troubleshooting.
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Scanning with the 180 kV nano-focus tube
By April Neander, The University of Chicago
Chapter 8 of the University of Chicago PaleoCT training course. Covers the differences between the 240 kV micro-focus and 180 kV nano-focus tubes, mounting, positioning and parameters for lower density specimens, and additional focus tools.
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Fossils and Filters
By April Neander, The University of Chicago
Chapter 7 of the University of Chicago PaleoCT training course. Covers tips for mounting fossils, and when and how to use filters.
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Scanning with the High Power 240 kV Tube
By April Neander, The University of Chicago
Chapter 6 of the University of Chicago PaleoCT training course. Covers scanning software for Waygate machines, positioning a specimen in the scanner, how to read a histogram, scanning parameters, and detector calibration.
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Pre-Scan
By April Neander, The University of Chicago
Chapter 5 of the University of Chicago PaleoCT training course. This video covers power modes, changing a dual tube system, and warmup. This video is specific to Phoenix/GE/Waygate machines.
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Mounting Specimens
By April Neander, The University of Chicago
Chapter 4 of the University of Chicago PaleoCT training course. Covers intro to mounting and wet specimens.
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Background and Theory
By April Neander, The University of Chicago
Chapter 3 of the University of Chicago PaleoCT training course. Covers basic vocabulary, parts of the machine, common artefacts, and quality/speed/resolution tradeoffs.
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Introduction to Micro-CT Scanning
By April Neander, The University of Chicago
Introductory video for the University of Chicago PaleoCT facility. Covers basic vocabulary, parts of the machine, mounting, common artefacts, and quality/speed/resolution tradeoffs.
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Basics and Physics of X-Ray Imaging & 3D Computed Tomography (Volume Graphics)
By S. Gondrom-Linke, Volume Graphics
https://www.dropbox.com/s/zlvqvtklmqdu3d3/Physics%20and%203DCT.pdf?dl=0
CT history, basics, how a CT scanning and reconstruction works with relevant mathematical explanations, and demonstration of how VGStudio Reconstruction can be used to correct artifacts.
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NC State University Analytical Instrument Facility: Short Introduction to X-ray Computed Tomography
Video about basics of how CT works.
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Forelimb homology 3D model collection
By Jaimi Gray, UTCT, University of Texas
http://www.graysvertebrateanatomy.com/work/forelimbhomology/
A collection of colorized skeletal forelimb models from the vertebrate tree of life.
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The Virtual Paleontologist
By Anne Kort, University of Michigan
https://www.youtube.com/@VirtPaleo
Comprehensive tutorials about using, processing, and analyzing CT data primarily focused on the field of Paleontology.
3D Slicer, Blender, Data Analysis, Data Postprocessing, MeshLab, Reconstruction, Segmenting, YouTube Channel
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X-ray computed tomography of planetary materials: A primer and review of recent studies
Hanna, Romy D., and Richard A. Ketcham. “X-ray computed tomography of planetary materials: A primer and review of recent studies.” Geochemistry 77, no. 4 (2017): 547-572. https://doi.org/10.1016/j.chemer.2017.01.006
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Enhancing CT imaging: A safe protocol to stain and de-stain rare fetal museum specimens using diffusible iodine-based staining (diceCT)
Lanzetti, Agnese, and Eric G. Ekdale. “Enhancing CT imaging: A safe protocol to stain and de‐stain rare fetal museum specimens using diffusible iodine‐based staining (diceCT).” Journal of Anatomy 239, no. 1 (2021): 228-241. https://doi.org/10.1111/joa.13410
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Experimental assessment of diffusible iodine-based contrast-enhanced computed tomography (diceCT) protocols
Costello, Lucy F., Hazel L. Richards, Alistair R. Evans, and Justin W. Adams. “Experimental assessment of diffusible iodine-based contrast-enhanced computed tomography (diceCT) protocols.” PeerJ 12 (2024): e17919. https://doi.org/10.7717/peerj.17919