scholarly journals A 3D adult zebrafish brain atlas (AZBA) for the digital age

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Justin W Kenney ◽  
Patrick E Steadman ◽  
Olivia Young ◽  
Meng Ting Shi ◽  
Maris Polanco ◽  
...  

Zebrafish have made significant contributions to our understanding of the vertebrate brain and the neural basis of behavior, earning a place as one of the most widely used model organisms in neuroscience. Their appeal arises from the marriage of low cost, early life transparency, and ease of genetic manipulation with a behavioral repertoire that becomes more sophisticated as animals transition from larvae to adults. To further enhance the use of adult zebrafish, we created the first fully segmented three-dimensional digital adult zebrafish brain atlas (AZBA). AZBA was built by combining tissue clearing, light-sheet fluorescence microscopy, and three-dimensional image registration of nuclear and antibody stains. These images were used to guide segmentation of the atlas into over 200 neuroanatomical regions comprising the entirety of the adult zebrafish brain. As an open source, online (azba.wayne.edu), updatable digital resource, AZBA will significantly enhance the use of adult zebrafish in furthering our understanding of vertebrate brain function in both health and disease.

2010 ◽  
Vol 8 (56) ◽  
pp. 395-409 ◽  
Author(s):  
Andrew D. Straw ◽  
Kristin Branson ◽  
Titus R. Neumann ◽  
Michael H. Dickinson

Automated tracking of animal movement allows analyses that would not otherwise be possible by providing great quantities of data. The additional capability of tracking in real time—with minimal latency—opens up the experimental possibility of manipulating sensory feedback, thus allowing detailed explorations of the neural basis for control of behaviour. Here, we describe a system capable of tracking the three-dimensional position and body orientation of animals such as flies and birds. The system operates with less than 40 ms latency and can track multiple animals simultaneously. To achieve these results, a multi-target tracking algorithm was developed based on the extended Kalman filter and the nearest neighbour standard filter data association algorithm. In one implementation, an 11-camera system is capable of tracking three flies simultaneously at 60 frames per second using a gigabit network of nine standard Intel Pentium 4 and Core 2 Duo computers. This manuscript presents the rationale and details of the algorithms employed and shows three implementations of the system. An experiment was performed using the tracking system to measure the effect of visual contrast on the flight speed of Drosophila melanogaster . At low contrasts, speed is more variable and faster on average than at high contrasts. Thus, the system is already a useful tool to study the neurobiology and behaviour of freely flying animals. If combined with other techniques, such as ‘virtual reality’-type computer graphics or genetic manipulation, the tracking system would offer a powerful new way to investigate the biology of flying animals.


2020 ◽  
Vol 64 (5) ◽  
pp. 50405-1-50405-5
Author(s):  
Young-Woo Park ◽  
Myounggyu Noh

Abstract Recently, the three-dimensional (3D) printing technique has attracted much attention for creating objects of arbitrary shape and manufacturing. For the first time, in this work, we present the fabrication of an inkjet printed low-cost 3D temperature sensor on a 3D-shaped thermoplastic substrate suitable for packaging, flexible electronics, and other printed applications. The design, fabrication, and testing of a 3D printed temperature sensor are presented. The sensor pattern is designed using a computer-aided design program and fabricated by drop-on-demand inkjet printing using a magnetostrictive inkjet printhead at room temperature. The sensor pattern is printed using commercially available conductive silver nanoparticle ink. A moving speed of 90 mm/min is chosen to print the sensor pattern. The inkjet printed temperature sensor is demonstrated, and it is characterized by good electrical properties, exhibiting good sensitivity and linearity. The results indicate that 3D inkjet printing technology may have great potential for applications in sensor fabrication.


2017 ◽  
Vol 68 (3) ◽  
pp. 453-458 ◽  
Author(s):  
Daniel Besnea ◽  
Alina Spanu ◽  
Iuliana Marlena Prodea ◽  
Gheorghita Tomescu ◽  
Iolanda Constanta Panait

The paper points out the advantages of rapid prototyping for improving the performances/constructive optimization of mixing devices used in process industries, here exemplified to propeller types ones. The multidisciplinary optimization of the propeller profile affords its design using parametric CAD methods. Starting from the mathematical curve equations proposed for the blade profile, it was determined its three-dimensional virtual model. The challenge has been focused on the variation of propeller pitch and external diameter. Three dimensional ranges were manufactured using the additive manufacturing process with Marker Boot 3D printer. The mixing performances were tested on the mixing equipment measuring the minimum rotational speed and the correspondent shaft torque for complete suspension achieved for each of the three models. The virtual and rapid prototyping method is newly proposed by the authors to obtain the basic data for scale up of the mixing systems, in the case of flexible production (of low quantities), in which both the nature and concentration of the constituents in the final product varies often. It is an efficient and low cost method for the rapid identification of the optimal mixing device configuration, which contributes to the costs reduction and to the growing of the output.


2021 ◽  
Vol 10 (7) ◽  
pp. 460
Author(s):  
Mario Matthys ◽  
Laure De Cock ◽  
John Vermaut ◽  
Nico Van de Weghe ◽  
Philippe De Maeyer

More and more digital 3D city models might evolve into spatiotemporal instruments with time as the 4th dimension. For digitizing the current situation, 3D scanning and photography are suitable tools. The spatial future could be integrated using 3D drawings by public space designers and architects. The digital spatial reconstruction of lost historical environments is more complex, expensive and rarely done. Three-dimensional co-creative digital drawing with citizens’ collaboration could be a solution. In 2016, the City of Ghent (Belgium) launched the “3D city game Ghent” project with time as one of the topics, focusing on the reconstruction of disappeared environments. Ghent inhabitants modelled in open-source 3D software and added animated 3D gamification and Transmedia Storytelling, resulting in a 4D web environment and VR/AR/XR applications. This study analyses this low-cost interdisciplinary 3D co-creative process and offers a framework to enable other cities and municipalities to realise a parallel virtual universe (an animated digital twin bringing the past to life). The result of this co-creation is the start of an “Animated Spatial Time Machine” (AniSTMa), a term that was, to the best of our knowledge, never used before. This research ultimately introduces a conceptual 4D space–time diagram with a relation between the current physical situation and a growing number of 3D animated models over time.


2012 ◽  
Vol 497 ◽  
pp. 89-93
Author(s):  
Liang Liang Yuan ◽  
Ke Hua Zhang ◽  
Li Min

In order to process heterotype hole of workpiece precisely, an open abrasive flow polish machine is designed, and the optimization design of machine frame is done for low cost. Firstly, basing on the parameters designed with traditional ways, three-dimensional force model is set up with the soft of SolidWorks. Secondly, the statics and modal analysis for machine body have been done in Finite element methods (FEM), and then the optimization analysis of machine frame has been done. At last, the model of rebuild machine frame has been built. Result shows that the deformation angle value of machine frame increased from 0.72′ to 1.001′, the natural frequency of the machine decreased from 75.549 Hz to 62.262 Hz, the weight of machine decreased by 74.178 Kg after optimization. It meets the strength, stiffness and angel stiffness requirement of machine, reduces the weight and cost of machine.


Cells ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 637
Author(s):  
Nicholas S. Moore ◽  
Robert A. Mans ◽  
Mackenzee K. McCauley ◽  
Colton S. Allgood ◽  
Keri A. Barksdale

Evidence from human and animal studies indicate that disrupted light cycles leads to alterations of the sleep state, poor cognition, and the risk of developing neuroinflammatory and generalized health disorders. Zebrafish exhibit a diurnal circadian rhythm and are an increasingly popular model in studies of neurophysiology and neuropathophysiology. Here, we investigate the effect of alterations in light cycle on the adult zebrafish brain: we measured the effect of altered, unpredictable light exposure in adult zebrafish telencephalon, homologous to mammalian hippocampus, and the optic tectum, a significant visual processing center with extensive telencephalon connections. The expression of heat shock protein-70 (HSP70), an important cell stress mediator, was significantly decreased in optic tectum of adult zebrafish brain following four days of altered light exposure. Further, pSer473-Akt (protein kinase B) was significantly reduced in telencephalon following light cycle alteration, and pSer9-GSK3β (glycogen synthase kinase-3β) was significantly reduced in both the telencephalon and optic tectum of light-altered fish. Animals exposed to five minutes of environmental enrichment showed significant increase in pSer473Akt, which was significantly attenuated by four days of altered light exposure. These data show for the first time that unpredictable light exposure alters HSP70 expression and dysregulates Akt-GSK3β signaling in the adult zebrafish brain.


Nanomaterials ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1145
Author(s):  
Prem. C. Pandey ◽  
Shubhangi Shukla ◽  
Roger J. Narayan

Prussian blue nanoparticles (PBN) exhibit selective fluorescence quenching behavior with heavy metal ions; in addition, they possess characteristic oxidant properties both for liquid–liquid and liquid–solid interface catalysis. Here, we propose to study the detection and efficient removal of toxic arsenic(III) species by materializing these dual functions of PBN. A sophisticated PBN-sensitized fluorometric switching system for dosage-dependent detection of As3+ along with PBN-integrated SiO2 platforms as a column adsorbent for biphasic oxidation and elimination of As3+ have been developed. Colloidal PBN were obtained by a facile two-step process involving chemical reduction in the presence of 2-(3,4-epoxycyclohexyl)ethyl trimethoxysilane (EETMSi) and cyclohexanone as reducing agents, while heterogeneous systems were formulated via EETMSi, which triggered in situ growth of PBN inside the three-dimensional framework of silica gel and silica nanoparticles (SiO2). PBN-induced quenching of the emission signal was recorded with an As3+ concentration (0.05–1.6 ppm)-dependent fluorometric titration system, owing to the potential excitation window of PBN (at 480–500 nm), which ultimately restricts the radiative energy transfer. The detection limit for this arrangement is estimated around 0.025 ppm. Furthermore, the mesoporous and macroporous PBN-integrated SiO2 arrangements might act as stationary phase in chromatographic studies to significantly remove As3+. Besides physisorption, significant electron exchange between Fe3+/Fe2+ lattice points and As3+ ions enable complete conversion to less toxic As5+ ions with the repeated influx of mobile phase. PBN-integrated SiO2 matrices were successfully restored after segregating the target ions. This study indicates that PBN and PBN-integrated SiO2 platforms may enable straightforward and low-cost removal of arsenic from contaminated water.


2021 ◽  
Vol 11 (12) ◽  
pp. 5321
Author(s):  
Marcin Barszcz ◽  
Jerzy Montusiewicz ◽  
Magdalena Paśnikowska-Łukaszuk ◽  
Anna Sałamacha

In the era of the global pandemic caused by the COVID-19 virus, 3D digitisation of selected museum artefacts is becoming more and more frequent practice, but the vast majority is performed by specialised teams. The paper presents the results of comparative studies of 3D digital models of the same museum artefacts from the Silk Road area generated by two completely different technologies: Structure from Motion (SfM)—a method belonging to the so-called low-cost technologies—and by Structured-light 3D Scanning (3D SLS). Moreover, procedural differences in data acquisition and their processing to generate three-dimensional models are presented. Models built using a point cloud were created from data collected in the Afrasiyab museum in Samarkand (Uzbekistan) during “The 1st Scientific Expedition of the Lublin University of Technology to Central Asia” in 2017. Photos for creating 3D models in SfM technology were taken during a virtual expedition carried out under the “3D Digital Silk Road” program in 2021. The obtained results show that the quality of the 3D models generated with SfM differs from the models from the technology (3D SLS), but they may be placed in the galleries of the vitrual museum. The obtained models from SfM do not have information about their size, which means that they are not fully suitable for archiving purposes of cultural heritage, unlike the models from SLS.


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