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Fig. 8 in A new subdisarticulated machaeridian from the Middle Devonian of China: Insights into taphonomy and taxonomy using X-ray microtomography and 3D-analysis

Fig. 8. Orientation of the 70 dacryoconarids in the sample. A. Rose diagram showing the lineations of the dacryoconarids (numbers 5 and 8 refer to dacryoconarid counts; note that both the tip and aperture where counted of each object resulting in double counts). B. Rose diagram showing dacryoconarids whose apices are higher (open rectangles) and lower (closed rectangles) positioned than their corresponding open ends in relation to an imagined x-y-plane.

Fig. 9 in A new subdisarticulated machaeridian from the Middle Devonian of China: Insights into taphonomy and taxonomy using X-ray microtomography and 3D-analysis

Fig. 9. Comparison between the known species of Lepidocoleus and L. kuangguoduni sp. nov. with number of sclerites, age, and geographic occurrence indicated; lateral (A) and dorsal (E) views of the fossils, images of sclerites (B), outlines of sclerites (C), cross sections, to show the proportions of the dorsal depression (D).

Fig. 4 in A new subdisarticulated machaeridian from the Middle Devonian of China: Insights into taphonomy and taxonomy using X-ray microtomography and 3D-analysis

Fig. 4. Overview of the almost complete sclerites from the 3D-analysis (orthographic perspective). Group I: sclerites 1, 4, 6 (A–C) and group II: sclerites 2, 5, 7, 10 (D–G). Internal (A1–G1), lateral (A2–G2), dorsal (A3–G3), posterior (A4–G4), and anterior (A5–G5) views.

Fig. 7 in A new subdisarticulated machaeridian from the Middle Devonian of China: Insights into taphonomy and taxonomy using X-ray microtomography and 3D-analysis

Fig. 7. Overview of objects interpreted as dacryoconarids surrounding the machaeridian sclerites. A. All objects including the ones discarded for further analysis (light grey). B. Dacryoconarids selected for measurements (red).

Fig. 3 in A new subdisarticulated machaeridian from the Middle Devonian of China: Insights into taphonomy and taxonomy using X-ray microtomography and 3D-analysis

Fig. 3. Overview over the assemblage of the sixteen 3D-objects which were created from different viewpoints. Orthographic top (A) and front (B) views. Orthographic top view (C), projected on the sample to show the position of the 3D-model in the correct position on the x-y-plane and corresponding viewing directions. Orthographic left side (D) and right side (E) views.

Fig. 7. 3D in A new beaked whale record from the upper Miocene of Menorca, Balearic Islands, based on CT-scan analysis of limestone slabs

Fig. 7. 3D reconstruction resulting from the CT-scan of the ziphiid cetacean Messapicetus cf. longirostris Bianucci, Landini, and Varola, 1992 skull MDM-2029) inside two limestone slabs from the Tortonian of Menorca (Balearic Islands, Spain); in left lateral view (A1), left lateral view without the mandibles (A2), detail of the orbital area (A3).

Fig. 6. 3D in A new beaked whale record from the upper Miocene of Menorca, Balearic Islands, based on CT-scan analysis of limestone slabs

Fig. 6. 3D reconstruction resulting from the CT-scan of the ziphiid cetacean Messapicetus cf. longirostris Bianucci, Landini, and Varola, 1992 skull (MDM-2029) inside two limestone slabs from the Tortonian of Menorca (Balearic Islands, Spain); in right lateral view (A1), right lateral view without the mandibles (A2), detail of the pterygoid hamuli showing the well-preserved transverse crests (A3).

Fig. 4. 3D in A new beaked whale record from the upper Miocene of Menorca, Balearic Islands, based on CT-scan analysis of limestone slabs

Fig. 4. 3D reconstruction resulting from the CT-scan of the ziphiid cetacean Messapicetus cf. longirostris Bianucci, Landini, and Varola, 1992 skull (MDM-2029) inside two limestone slabs from the Tortonian of Menorca (Balearic Islands, Spain); in anterior view, showing transverse cross sections of the rostrum (A1–A4) made at different distances from the rostrum base. Not to scale.

Fig. 3. 3D in A new beaked whale record from the upper Miocene of Menorca, Balearic Islands, based on CT-scan analysis of limestone slabs

Fig. 3. 3D reconstruction resulting from the CT-scan of the ziphiid cetacean Messapicetus cf. longirostris Bianucci, Landini, and Varola, 1992 skull MDM-2029) inside two limestone slabs from the Tortonian of Menorca (Balearic Islands, Spain), in dorsal (A1) and anterodorsal (A2) views.

Fig. 5. 3D in A new beaked whale record from the upper Miocene of Menorca, Balearic Islands, based on CT-scan analysis of limestone slabs

Fig. 5. 3D reconstruction resulting from the CT-scan of the ziphiid cetacean Messapicetus cf. longirostris Bianucci, Landini, and Varola, 1992 skull (MDM- 2029) inside two limestone slabs from the Tortonian of Menorca (Balearic Islands, Spain); in ventral view (A1), ventral view without the mandibles (A2).

opencc-by-4.0Nov 2024View details →

3D Printing Simulation Analysis of skeleton gyroid structure (standard, double and graded)_Spoke11_WP4_Task4.1_MOST

These findings provide a comprehensive understanding of the challenges and considerations in 3D printing complex lattice structures, emphasizing the importance of residual stress management, thermal stability, and print direction alignment for optimal mechanical performance.

opencc-zeroDec 2009View details →

FIG. 3 in (Mammalia, Primates, Hominoidea): virtual reconstruction and 3D analysis of a juvenile mandibular dentition (RPl-82 and RPl-83)

FIG. 3. — μCT-based comparative enamel thickness and dentine shape variation of the lower deciduous second molar (m2) and permanent first molar (M1) in Ouranopithecus Bonis & Melentis, 1877, Homo Linnaeus, 1758, Pan Oken, 1816, and Gorilla Saint-Hillaire, 1853. Crowns have been digitally isolated from roots and are shown in lingual, occlusal, and buccal views. The enamel thickness topographic variation (upper row for each taxon) is rendered by a thickness-related grey scale (ranging from "thin" light to "thick" dark), specific for each investigated tooth. Isolated dark spots correspond to cuspal dental wear. Dentine partial volume (lower rows) is virtually rendered by enamel transparency. Scale bar: 5 mm.

opencc-zeroDec 2009View details →

FIG. 1 in (Mammalia, Primates, Hominoidea): virtual reconstruction and 3D analysis of a juvenile mandibular dentition (RPl-82 and RPl-83)

FIG. 1. — μCT-based 3D virtual reconstruction of the juvenile Ouranopithecus Bonis & Melentis, 1977 partial mandible bearing a mixed dentition from the late Miocene site of Ravin de la Pluie (Macedonia, Greece). The two portions, RPl-82 (left partial ramus) and RPl-83 (right partial ramus), are here shown in frontal view: A, RPl-83; B, RPl-82; C, D, RPl-83 and RPl-82 rendered in semi-transparency with indication of the deciduous and permanent dental elements preserved in situ. Abbreviations: see text. Scale bar: 10 mm.

opencc-zeroDec 2009View details →

FIG. 2 in (Mammalia, Primates, Hominoidea): virtual reconstruction and 3D analysis of a juvenile mandibular dentition (RPl-82 and RPl-83)

FIG. 2. — μCT-based virtual sections of six deciduous (Li2, Lc, Rc, Lm1, Rm1, Rm2) and eight permanent tooth crowns (LI2, RI2, LC, RC, LP3, RP3, RP4, RM1) from the juvenile Ouranopithecus Bonis & Melentis, 1977 partial mandible (RPl-82 and RPl-83). Abbreviations: see text; BL, buccolingual; BLm, buccolingual through the mesial cusps; BLd, buccolingual through the distal cusps; MD, mediodistal; MDl, mesiodistal through the lingual cusps; MDb, mesiodistal through the buccal cusps. Scale bar: 1 cm.

opencc-by-4.0Jan 2023View details →

Data and statistical analysis scripts for manuscript on pennycress roots & response to nitrate using 3D gel system

Data and statistical analysis scripts for manuscript on pennycress roots & response to nitrate using 3Dgel system <blockquote> A temporal analysis and response to nitrate availability of 3D root system architecture in diverse pennycress (Thlaspi arvense L.) accessions - [<a href="https://doi.org/10.3389/fpls.2023.1145389">https://doi.org/10.3389/fpls.2023.1145389</a>] </blockquote> The following files contains: <ul> <li><code>gel_data_preprocessing_20221024.R</code> - R statistics script for pre-processing data files from 3Dgel system GIARoots & DynamicRoots raw output</li> <li><code>gel_dataprocessing_20221229.R</code> - R statistics script for data processing of pre-processed 3D gel data</li> <li><code>TaGNS_N_Spring32.zip</code> -  CSV data files and R statistics script for Spring32 grown under high, low, trace and zero N treatments.</li> <li><code>TaGNE_N_Accessions.zip</code> - CSV data files and R statistics script for 3 accessions under high and trace N treatments.</li> <li><code>TaGAA_N_Accessions.zip</code> - CSV data files and R statistics script for 24 diverse pennycress lines grown under high N conditions.</li> </ul>

opencc-by-sa-4.0Mar 2016View details →

PanDDA analysis of BRD1 screened against 3D-Fragment-Consortium Fragment Library

Bromodomain BRD1 screened against the 3D Fragment Consortium Fragment Library by X-ray Crystallography.

opencc-by-4.0Apr 2024View details →

Beyond the Surface: Exploring Ancient Plant Food Processing through Confocal Microscopy and 3D Surface Texture Analysis

This repository contains the raw data and code to reproduce the analyses presented in the paper "Beyond the Surface: Exploring Ancient Plant Food Processing through Confocal Microscopy and 3D Surface Texture Analysis" by Zupancich et al. The repositiory includes: <ul> <li>CSV files containing the raw data of 3D surface measurement of experimental active and passive tools utilised in processing cereals and legumes.</li> <li>Rmarkdown files of the code utilised to perform the analyses</li> </ul>

dryad36/100

BEHAV3D: A 3D live imaging platform for comprehensive analysis of engineered T cell behavior and tumor response

The use of patient-derived material and immune cell co-cultures in modeling immune-oncology has gained significant interest for understanding and manipulating immune cell tumor targeting in a patient-specific context. However, current protocols have limitations in visualizing and analyzing the dynamic cellular features of these living culture systems. We recently developped a workflow names BEHAV3D, that combines multi-color live 3D imaging and computational tools to analyze cell death dynamics, classify T cell behavior, and generate data-informed 3D images and videos. Here we provide some example pre-processed dataset of videos of two co-culture set ups: breast cancer Patient Derived Organoids with αβ T cells engineered to express a γδ TCR (TEGs) and Acute Lymphoblastic Leukemia cells with CD19 CART cells.

opencc-zeroSep 2023View details →

opencc-by-4.0Mar 2022View details →

Research compendium for 'Practical and technical aspects for the 3D scanning of lithic artefacts using micro-computed tomography techniques and laser light scanners for subsequent geometric morphometric analysis. Introducing the StyroStone protocol'

Abstract: Here, we present a new method to scan a large number of lithic artefacts using three-dimensional (3D) scanning technology. Despite the rising use of high-resolution 3D surface scanners in archaeological sciences, no virtual studies have focused on the 3D digitization and analysis of small lithic implements such as bladelets, microblades, and microflakes. This is mostly due to difficulties in creating reliable 3D meshes of these artefacts resulting from several inherent features (i.e., size, translucency, and acute edge angles), which compromise the efficiency of structured light or laser scanners and photogrammetry. Our new protocol StyroStone addresses this problem by proposing a step-by-step procedure relying on the use of micro-computed tomographic technology, which is able to capture the 3D shape of small lithic implements in high detail. We tested a system that enables us to scan hundreds of artefacts together at once within a single scanning session lasting a few hours. As also bigger lithic artefacts (i.e., blades) are present in our sample, this protocol is complemented by a short guide on how to effectively scan such artefacts using a structured light scanner (Artec Space Spider). Furthermore, we estimate the accuracy of our scanning protocol using principal component analysis of 3D Procrustes shape coordinates on a sample of meshes of bladelets obtained with both micro-computed tomography and another scanning device (i.e., Artec Micro). A comprehensive review on the use of 3D geometric morphometrics in lithic analysis and other computer-based approaches is provided in the introductory chapter to show the advantages of improving 3D scanning protocols and increasing the digitization of our prehistoric human heritage. Content List: <ul> <li>S1. Step-by-step protocol entitled ‘StyroStone: A protocol for scanning and extracting three-dimensional meshes of stone artefacts using Micro-CT scanners’. Also available on protocols.io (dx.doi.org/10.17504/protocols.io.bzbfp2jn);</li> <li>S2. Dataset with all raw semilandmark coordinate data (in .xlsx format) used in the validation study;</li> <li>S3. AGMT3D project. The file “Validation Protocol-MorphoProject.mat” can be used to open the project in the software AGMT3D;</li> <li>S4. Dataset in .csv format of the principal component score data of the validation study;</li> <li>S5. R script used to create Figure 2 using the R package ggplot2;</li> <li>S6. 3D models of the experimental bladelets obtained with the Micro-CT scanner used in the validation study. Both .ply and .wrl formats are provided;</li> <li>S7. 3D models of the experimental bladelets obtained with the Artec Micro scanner used in the validation study. Both .ply and .wrl formats are provided.</li> </ul>