Microfocus X-ray CT (microCT) Imaging of Actinia equina (Cnidaria), Harmothoe sp. (Annelida), and Xenoturbella japonica (Xenacoelomorpha)

10.3791/59161 ◽  
2019 ◽  
Author(s):  
Akiteru Maeno ◽  
Hisanori Kohtsuka ◽  
Kensuke Takatani ◽  
Hiroaki Nakano
Keyword(s):  
X Ray ◽  
Microct Imaging

scholarly journals Emergent honeycomb topology of the leaf spongy mesophyll

2019 ◽  
Author(s):  
Aleca M. Borsuk ◽  
Adam B. Roddy ◽  
Guillaume Théroux-Rancourt ◽  
Craig R. Brodersen
Keyword(s):  
Vascular Plants ◽  
Scaling Laws ◽  
Allometric Scaling ◽  
Photosynthetic Performance ◽  
High Cell ◽  
Spongy Mesophyll ◽  
X Ray ◽  
Resource Investment ◽  
Mesophyll Structure ◽  
Microct Imaging

AbstractThe spongy mesophyll layer in leaves is ubiquitous among vascular plants, yet its structure is relatively unknown and typically described as a disordered assemblage of isodiametric cells. We characterized spongy mesophyll structure among diverse taxa using X-ray microCT imaging and found that leaves with small cell sizes, high cell packing densities, and close vein spacing were congruent with the isodiametric paradigm. When these structural traits exceeded well-defined thresholds, the spongy mesophyll domain was instead tessellated with an emergent topological motif of an irregular honeycomb that minimizes cellular investment and obeys Euler’s Law of space filling. Our data suggest spongy mesophyll is governed by allometric scaling laws, with two distinct topologies optimized for either photosynthetic performance or minimal resource investment.One Sentence SummaryConserved topological motifs in the spongy mesophyll are coordinated with leaf photosynthetic performance.

scholarly journals Digitally Deconstructing Leaves in 3D Using X-ray Microcomputed Tomography and Machine Learning

2019 ◽  
Author(s):  
Guillaume Théroux-Rancourt ◽  
Matthew R. Jenkins ◽  
Craig R. Brodersen ◽  
Andrew McElrone ◽  
Elisabeth J. Forrestel ◽  
...  
Keyword(s):  
Machine Learning ◽  
Microcomputed Tomography ◽  
Plant Phenotyping ◽  
3D Segmentation ◽  
Tissue Segmentation ◽  
Holistic View ◽  
X Ray ◽  
Single Leaf ◽  
Time Required ◽  
Microct Imaging

ABSTRACTPremise of the studyX-ray microcomputed tomography (microCT) can be used to measure 3D leaf internal anatomy, providing a holistic view of tissue organisation. Previously, the substantial time needed for segmenting multiple tissues limited this technique to small datasets, restricting its utility for phenotyping experiments and limiting our confidence in the conclusion of these studies due to low replication numbers.Methods and ResultsWe present a Python codebase for random-forest machine learning segmentation and 3D leaf anatomical trait quantification which dramatically reduces the time required to process single leaf microCT scans into detailed segmentations. By training the model on each scan using 6 hand segmented image slices out of >1500 in the full leaf scan, it achieves >90% accuracy in background and tissue segmentation.ConclusionOverall, this 3D segmentation and quantification pipeline can reduce one of the major barriers to using microCT imaging in high-throughput plant phenotyping.

Wormhole Growth in Dissolving Limestones: Insights from 4D Tomography

2021 ◽  
Author(s):  
Piotr Szymczak ◽  
Max P Cooper ◽  
Silvana Magni ◽  
Rishabh P Sharma ◽  
Tomasz P Blach ◽  
...  
Keyword(s):  
Fluid Transport ◽  
Mineral Surfaces ◽  
X Ray ◽  
Permeability Changes ◽  
Highly Nonlinear ◽  
Tomographic Data ◽  
Tip Position ◽  
Microct Imaging ◽  
The Impact

<p>Dissolution of porous media introduces a positive feedback between fluid transport and chemical reactions at mineral surfaces leading to the formation of pronounced wormhole-like channels. While the impact of flow rate and reaction rate on the shapes of the wormholes is now well understood, much less is known about the dynamics of their propagation. In this study we capture the evolution of wormholes and their effects on flow patterns by in-situ X-ray microCT imaging of dissolving limestone cores. 4D tomography allows us in particular to correlate the permeability changes in a dissolving core with the advancement of the tip position of the wormhole. Surprisingly, we find that the relation between the two is highly nonlinear, with extensive periods of relatively fast growth of the wormhole which is nevertheless not reflected in any significant change in the overall permeability.  We hypothesize that this is caused by the presence of highly cemented regions in the core which act as permeability barriers for the flow. The presence of such regions is confirmed by a detailed analysis of the pore geometry based on the tomographic data. The results demonstrate that the analysis of the wormhole dynamics in 4d tomography can be used to probe the internal structure of the rock. </p>

scholarly journals X-ray MicroCT Imaging of Dentin Tubules in a Human Tooth

2020 ◽  
Vol 26 (S2) ◽  
pp. 998-1000
Author(s):  
Carley Goodwin ◽  
Stephen Boona ◽  
Buwei Chen ◽  
Oliver Hesmondhalgh ◽  
Shaz Khan ◽  
...  
Keyword(s):  
Human Tooth ◽  
X Ray ◽  
Dentin Tubules ◽  
Microct Imaging

scholarly journals A correlation analysis of Light Microscopy and X-ray MicroCT imaging methods applied to archaeological plant remains’ morphological attributes visualization

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Cristina Marilin Calo ◽  
Marcia A. Rizzutto ◽  
Sandra M. Carmello-Guerreiro ◽  
Carlos S. B. Dias ◽  
Jennifer Watling ◽  
...  
Keyword(s):  
Light Microscopy ◽  
Archaeological Site ◽  
Micro Computed Tomography ◽  
Imaging Methods ◽  
X Ray ◽  
Plant Remains ◽  
Secretory Cavities ◽  
Definition Of ◽  
Microct Imaging ◽  
Non Destructive

Abstract In this work, several attributes of the internal morphology of drupaceous fruits found in the archaeological site Monte Castelo (Rondonia, Brazil) are analyzed by means of two different imaging methods. The aim is to explore similarities and differences in the visualization and analytical properties of the images obtained via High Resolution Light Microscopy and X-ray micro-computed tomography (X-ray MicroCT) methods. Both provide data about the three-layered pericarp (exo-, meso- and endocarp) of the studied exemplars, defined by cell differentiation, vascularisation, cellular contents, presence of sclerenchyma cells and secretory cavities. However, it is possible to identify a series of differences between the information that can be obtained through each of the methods. These variations are related to the definition of contours and fine details of some characteristics, their spatial distribution, size attributes, optical properties and material preservation. The results obtained from both imaging methods are complementary, contributing to a more exhaustive morphological study of the plant remains. X-ray MicroCT in phase-contrast mode represents a suitable non-destructive analytic technique when sample preservation is required.

scholarly journals In vivo quantification of plant starch reserves at micrometer resolution using X-ray microCT imaging and machine learning

2018 ◽  
Vol 218 (3) ◽  
pp. 1260-1269 ◽  
Author(s):  
J. Mason Earles ◽  
Thorsten Knipfer ◽  
Aude Tixier ◽  
Jessica Orozco ◽  
Clarissa Reyes ◽  
...  
Keyword(s):  
Machine Learning ◽  
X Ray ◽  
Microct Imaging

Study of plant remains from a fluvial shellmound (Monte Castelo, RO, Brazil) using the X-ray MicroCT imaging technique

2019 ◽  
Vol 26 ◽  
pp. 101902
Author(s):  
Cristina Marilin Calo ◽  
Marcia A. Rizzutto ◽  
Jennifer Watling ◽  
Laura Furquim ◽  
Myrtle P. Shock ◽  
...  
Keyword(s):  
Imaging Technique ◽  
X Ray ◽  
Plant Remains ◽  
Microct Imaging

scholarly journals Three-dimensional virtual histology enabled through cytoplasm-specific X-ray stain for microscopic and nanoscopic computed tomography

2018 ◽  
Vol 115 (10) ◽  
pp. 2293-2298 ◽  
Author(s):  
Madleen Busse ◽  
Mark Müller ◽  
Melanie A. Kimm ◽  
Simone Ferstl ◽  
Sebastian Allner ◽  
...  
Keyword(s):  
Staining Method ◽  
Tissue Sample ◽  
Three Dimensional ◽  
Tissue Samples ◽  
Diagnostic Screening ◽  
X Ray ◽  
Staining Protocol ◽  
Nondestructive Investigation ◽  
Microct Imaging ◽  
X Ray Absorption

Many histological methods require staining of the cytoplasm, which provides instrumental details for diagnosis. One major limitation is the production of 2D images obtained by destructive preparation of 3D tissue samples. X-ray absorption micro- and nanocomputed tomography (microCT and nanoCT) allows for a nondestructive investigation of a 3D tissue sample, and thus aids to determine regions of interest for further histological examinations. However, application of microCT and nanoCT to biological samples (e.g., biopsies) is limited by the missing contrast within soft tissue, which is important to visualize morphological details. We describe an eosin-based preparation overcoming the challenges of contrast enhancement and selectivity for certain tissues. The eosin-based staining protocol is suitable for whole-organ staining, which then enables high-resolution microCT imaging of whole organs and nanoCT imaging of smaller tissue pieces retrieved from the original sample. Our results demonstrate suitability of the eosin-based staining method for diagnostic screening of 3D tissue samples without impeding further diagnostics through histological methods.

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