Gigapixel behavioral and neural activity imaging with a novel multi-camera array microscope

The dynamics of living organisms are organized across many spatial scales, yet existing, cost-effective imaging systems can measure only a subset of these scales at once. Here, we have created a scalable multi-camera array microscope (MCAM) that enables comprehensive high-resolution recording from multiple spatial scales simultaneously, ranging from cellular structures to large-group behavioral dynamics. By collecting data from up to 96 cameras, we computationally generate gigapixel-scale images and movies near cellular resolution and 5 um sensitivity over hundreds of square centimeters. This allows us to observe the behavior and fine anatomical features of numerous freely moving model organisms on multiple spatial scales, including larval zebrafish, fruit flies, nematodes, carpenter ants, and slime mold. The MCAM architecture allows stereoscopic tracking of the z-position of organisms using the overlapping field of view from adjacent cameras. Further, we demonstrate the ability to acquire dual color fluorescence video of multiple freely moving zebrafish, recording neural activity via ratiometric calcium imaging. Overall, the MCAM provides a powerful platform for investigating cellular and behavioral processes across a wide range of spatial scales, but without the bottlenecks imposed by single-camera image acquisition systems.

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Mechanisms of Genome Maintenance in Plants: Playing It Safe With Breaks and Bumps

Frontiers in Genetics ◽

10.3389/fgene.2021.675686 ◽

2021 ◽

Vol 12 ◽

Author(s):

Aamir Raina ◽

Parmeshwar K. Sahu ◽

Rafiul Amin Laskar ◽

Nitika Rajora ◽

Richa Sao ◽

...

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Plant Growth ◽

Genomic Instability ◽

Model Organisms ◽

Ultraviolet Rays ◽

Genomic Integrity ◽

Wide Range ◽

Repair Pathways ◽

Living Organisms

Maintenance of genomic integrity is critical for the perpetuation of all forms of life including humans. Living organisms are constantly exposed to stress from internal metabolic processes and external environmental sources causing damage to the DNA, thereby promoting genomic instability. To counter the deleterious effects of genomic instability, organisms have evolved general and specific DNA damage repair (DDR) pathways that act either independently or mutually to repair the DNA damage. The mechanisms by which various DNA repair pathways are activated have been fairly investigated in model organisms including bacteria, fungi, and mammals; however, very little is known regarding how plants sense and repair DNA damage. Plants being sessile are innately exposed to a wide range of DNA-damaging agents both from biotic and abiotic sources such as ultraviolet rays or metabolic by-products. To escape their harmful effects, plants also harbor highly conserved DDR pathways that share several components with the DDR machinery of other organisms. Maintenance of genomic integrity is key for plant survival due to lack of reserve germline as the derivation of the new plant occurs from the meristem. Untowardly, the accumulation of mutations in the meristem will result in a wide range of genetic abnormalities in new plants affecting plant growth development and crop yield. In this review, we will discuss various DNA repair pathways in plants and describe how the deficiency of each repair pathway affects plant growth and development.

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A simple, cost-effective, morphometric marker for characterising abalone populations at multiple spatial scales

Marine and Freshwater Research ◽

10.1071/mf07150 ◽

2008 ◽

Vol 59 (1) ◽

pp. 32 ◽

Cited By ~ 18

Author(s):

Thor M. Saunders ◽

Stephen Mayfield ◽

Andrew A. Hogg

Keyword(s):

Spatial Scales ◽

Shell Height ◽

South Australia ◽

Cost Effective ◽

Maximum Size ◽

Marine Species ◽

Isolated Populations ◽

Multiple Spatial Scales ◽

Lower Maximum ◽

Haliotis Rubra

The ability to identify and separately manage component populations is becoming increasingly important in guarding against overexploitation of many marine species. Blacklip abalone (Haliotis rubra) form isolated populations with variable life history characteristics as a result of the heterogenous areas they inhabit. Many of these populations are ‘stunted’, reaching a lower maximum size compared with those in adjacent areas. We obtained a range of morphological measurements from samples of ‘stunted’ and ‘non-stunted’ H. rubra collected from sites spread across broad (tens of kilometres) and fine (hundreds of metres) spatial scales in southern South Australia. The ratio between shell length and shell height showed clear and significant differences among samples from ‘stunted’ and ‘non-stunted’ sites. The morphometric collections from the sub-sites suggested that ‘stunted’ populations existed at smaller spatial scales (up to 400 m) compared with that for ‘non-stunted’ populations (at least 1000 m). The ‘morphometric marker’ developed in the present study has the potential to be used as a tool to identify individual populations rapidly and cost-effectively that can then be managed separately. Our approach is applicable to other species of abalone as well as other sedentary invertebrates with limited larval dispersal.

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Canopy Height Estimation from Single Multispectral 2D Airborne Imagery Using Texture Analysis and Machine Learning in Structurally Rich Temperate Forests

Remote Sensing ◽

10.3390/rs11232853 ◽

2019 ◽

Vol 11 (23) ◽

pp. 2853

Author(s):

Christos Boutsoukis ◽

Ioannis Manakos ◽

Marco Heurich ◽

Anastasios Delopoulos

Keyword(s):

Land Cover ◽

Texture Analysis ◽

Spatial Scales ◽

Computational Cost ◽

Texture Feature ◽

Cost Effective ◽

Canopy Height ◽

Support Vector ◽

Structural Parameter ◽

Wide Range

Canopy height is a fundamental biophysical and structural parameter, crucial for biodiversity monitoring, forest inventory and management, and a number of ecological and environmental studies and applications. It is a determinant for linking the classification of land cover to habitat categories towards building one-to-one relationships. Light detection and ranging (LiDAR) or 3D Stereoscopy are the commonly used and most accurate remote sensing approaches to measure canopy height. However, both require significant time and budget resources. This study proposes a cost-effective methodology for canopy height approximation using texture analysis on a single 2D image. An object-oriented approach is followed using land cover (LC) map as segmentation vector layer to delineate landscape objects. Global texture feature descriptors are calculated for each land cover object and used as variables in a number of classifiers, including single and ensemble trees, and support vector machines. The aim of the analysis is the discrimination among classes in a wide range of height values used for habitat mapping (from less than 5 cm to 40 m). For that task, different spatial resolutions are tested, representing a range from airborne to spaceborne quality ones, as well as their combinations, forming a multiresolution training set. Multiple dataset alternatives are formed based on the missing data handling, outlier removal, and data normalization techniques. The approach was applied using orthomosaics from DMC II airborne images, and evaluated against a reference LiDAR-derived canopy height model (CHM). Results reached overall object-based accuracies of 67% with the percentage of total area correctly classified exceeding 88%. Sentinel-2 simulation and multiresolution analysis (MRA) experiments achieved even higher accuracies of up to 85% and 91%, respectively, at reduced computational cost, showing potential in terms of transferability of the framework to large spatial scales.

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2D Color-Intensity Representation of Ultrasonic Thickness Gauge Measurements

Materials Evaluation ◽

10.32548/2020.me-04177 ◽

2020 ◽

pp. 1192-1198

Author(s):

M.S. Mohammad ◽

Tibebe Tesfaye ◽

Kim Ki-Seong

Keyword(s):

Cost Effective ◽

The Other ◽

Thickness Gauge ◽

Color Intensity ◽

Digital Readout ◽

Flat Surfaces ◽

Video Cameras ◽

Wide Range ◽

Cost Effective Alternative ◽

Ultrasonic Thickness

Ultrasonic thickness gauges are easy to operate and reliable, and can be used to measure a wide range of thicknesses and inspect all engineering materials. Supplementing the simple ultrasonic thickness gauges that present results in either a digital readout or as an A-scan with systems that enable correlating the measured values to their positions on the inspected surface to produce a two-dimensional (2D) thickness representation can extend their benefits and provide a cost-effective alternative to expensive advanced C-scan machines. In previous work, the authors introduced a system for the positioning and mapping of the values measured by the ultrasonic thickness gauges and flaw detectors (Tesfaye et al. 2019). The system is an alternative to the systems that use mechanical scanners, encoders, and sophisticated UT machines. It used a camera to record the probe’s movement and a projected laser grid obtained by a laser pattern generator to locate the probe on the inspected surface. In this paper, a novel system is proposed to be applied to flat surfaces, in addition to overcoming the other limitations posed due to the use of the laser projection. The proposed system uses two video cameras, one to monitor the probe’s movement on the inspected surface and the other to capture the corresponding digital readout of the thickness gauge. The acquired images of the probe’s position and thickness gauge readout are processed to plot the measured data in a 2D color-coded map. The system is meant to be simpler and more effective than the previous development.

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Inhibition of coral settlement at multiple spatial scales by a pervasive algal competitor

Marine Ecology Progress Series ◽

10.3354/meps12879 ◽

2019 ◽

Vol 612 ◽

pp. 29-42 ◽

Cited By ~ 4

Author(s):

NR Evensen ◽

C Doropoulos ◽

KM Morrow ◽

CA Motti ◽

PJ Mumby

Keyword(s):

Spatial Scales ◽

Coral Settlement ◽

Multiple Spatial Scales

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Worldview-2 and Landsat 8 Satellite Data for Seaweed Mapping along Karachi Coast

Pakistan Journal of Engineering Technology & Science ◽

10.22555/pjets.v5i2.920 ◽

2016 ◽

Vol 5 (2) ◽

Cited By ~ 1

Author(s):

Muhammad Danish Siddiqui ◽

Arjumand Z Zaidi

Keyword(s):

Satellite Data ◽

Spatial Scales ◽

Economic Value ◽

Vegetation Indices ◽

Cost Effective ◽

Geographical Information ◽

Landsat 8 ◽

Coverage Area ◽

Breeding Sites ◽

Marine Plant

Seaweed is a marine plant or algae which has economic value in many parts of the world. The purpose of this study is to evaluate different satellite sensors such as high-resolution WorldView-2 (WV2) satellite data and Landsat 8 30-meter resolution satellite data for mapping seaweed resources along the coastal waters of Karachi. The continuous monitoring and mapping of this precious marine plant and their breeding sites may not be very efficient and cost effective using traditional survey techniques. Remote Sensing (RS) and Geographical Information System (GIS) can provide economical and more efficient solutions for mapping and monitoring coastal resources quantitatively as well as qualitatively at both temporal and spatial scales. Normalized Difference Vegetation Indices (NDVI) along with the image enhancement techniques were used to delineate seaweed patches in the study area. The coverage area of seaweed estimated with WV-2 and Landsat 8 are presented as GIS maps. A more precise area estimation wasachieved with WV-2 data that shows 15.5Ha (0.155 Km2)of seaweed cover along Karachi coast that is more representative of the field observed data. A much larger area wasestimated with Landsat 8 image (71.28Ha or 0.7128 Km2) that was mainly due to the mixing of seaweed pixels with water pixels. The WV-2 data, due to its better spatial resolution than Landsat 8, have proven to be more useful than Landsat 8 in mapping seaweed patches

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The Future of Plasma-Based Surface Engineering Techniques in Tribology (Keynote)

World Tribology Congress III, Volume 2 ◽

10.1115/wtc2005-64180 ◽

2005 ◽

Cited By ~ 1

Author(s):

Allan Matthews ◽

Adrian Leyland

Keyword(s):

Surface Engineering ◽

Performance Enhancement ◽

Bulk Material ◽

Cost Savings ◽

Cost Effective ◽

Ceramic Coatings ◽

Performance Improvements ◽

Treatment Techniques ◽

Wide Range ◽

Macro Scale

Over the past twenty years or so, there have been major steps forward both in the understanding of tribological mechanisms and in the development of new coating and treatment techniques to better “engineer” surfaces to achieve reductions in wear and friction. Particularly in the coatings tribology field, improved techniques and theories which enable us to study and understand the mechanisms occurring at the “nano”, “micro” and “macro” scale have allowed considerable progress to be made in (for example) understanding contact mechanisms and the influence of “third bodies” [1–5]. Over the same period, we have seen the emergence of the discipline which we now call “Surface Engineering”, by which, ideally, a bulk material (the ‘substrate’) and a coating are combined in a way that provides a cost-effective performance enhancement of which neither would be capable without the presence of the other. It is probably fair to say that the emergence and recognition of Surface Engineering as a field in its own right has been driven largely by the availability of “plasma”-based coating and treatment processes, which can provide surface properties which were previously unachievable. In particular, plasma-assisted (PA) physical vapour deposition (PVD) techniques, allowing wear-resistant ceramic thin films such as titanium nitride (TiN) to be deposited on a wide range of industrial tooling, gave a step-change in industrial productivity and manufactured product quality, and caught the attention of engineers due to the remarkable cost savings and performance improvements obtained. Subsequently, so-called 2nd- and 3rd-generation ceramic coatings (with multilayered or nanocomposite structures) have recently been developed [6–9], to further extend tool performance — the objective typically being to increase coating hardness further, or extend hardness capabilities to higher temperatures.

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Gamma models for estimating the odds ratio for a skewed biomarker measured in pools and subject to errors

Biostatistics ◽

10.1093/biostatistics/kxz028 ◽

2019 ◽

Author(s):

Dane R Van Domelen ◽

Emily M Mitchell ◽

Neil J Perkins ◽

Enrique F Schisterman ◽

Amita K Manatunga ◽

...

Keyword(s):

Odds Ratio ◽

Adjusted Odds Ratio ◽

Lower Cost ◽

Cost Effective ◽

Ratio Estimation ◽

Statistical Efficiency ◽

Function Model ◽

Processing Error ◽

Wide Range ◽

Pooled Samples

SUMMARYMeasuring a biomarker in pooled samples from multiple cases or controls can lead to cost-effective estimation of a covariate-adjusted odds ratio, particularly for expensive assays. But pooled measurements may be affected by assay-related measurement error (ME) and/or pooling-related processing error (PE), which can induce bias if ignored. Building on recently developed methods for a normal biomarker subject to additive errors, we present two related estimators for a right-skewed biomarker subject to multiplicative errors: one based on logistic regression and the other based on a Gamma discriminant function model. Applied to a reproductive health dataset with a right-skewed cytokine measured in pools of size 1 and 2, both methods suggest no association with spontaneous abortion. The fitted models indicate little ME but fairly severe PE, the latter of which is much too large to ignore. Simulations mimicking these data with a non-unity odds ratio confirm validity of the estimators and illustrate how PE can detract from pooling-related gains in statistical efficiency. These methods address a key issue associated with the homogeneous pools study design and should facilitate valid odds ratio estimation at a lower cost in a wide range of scenarios.

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mtDNAcombine: tools to combine sequences from multiple studies

BMC Bioinformatics ◽

10.1186/s12859-021-04048-0 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Eleanor F. Miller ◽

Andrea Manica

Keyword(s):

Sequence Data ◽

Data Extraction ◽

Bayesian Skyline Plot ◽

Model Organisms ◽

Data Sets ◽

Data Handling ◽

Online Database ◽

Genetic Studies ◽

Wide Range ◽

Existing Data

Abstract Background Today an unprecedented amount of genetic sequence data is stored in publicly available repositories. For decades now, mitochondrial DNA (mtDNA) has been the workhorse of genetic studies, and as a result, there is a large volume of mtDNA data available in these repositories for a wide range of species. Indeed, whilst whole genome sequencing is an exciting prospect for the future, for most non-model organisms’ classical markers such as mtDNA remain widely used. By compiling existing data from multiple original studies, it is possible to build powerful new datasets capable of exploring many questions in ecology, evolution and conservation biology. One key question that these data can help inform is what happened in a species’ demographic past. However, compiling data in this manner is not trivial, there are many complexities associated with data extraction, data quality and data handling. Results Here we present the mtDNAcombine package, a collection of tools developed to manage some of the major decisions associated with handling multi-study sequence data with a particular focus on preparing sequence data for Bayesian skyline plot demographic reconstructions. Conclusions There is now more genetic information available than ever before and large meta-data sets offer great opportunities to explore new and exciting avenues of research. However, compiling multi-study datasets still remains a technically challenging prospect. The mtDNAcombine package provides a pipeline to streamline the process of downloading, curating, and analysing sequence data, guiding the process of compiling data sets from the online database GenBank.

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On the generation of internal waves by river plumes in subcritical initial conditions

Scientific Reports ◽

10.1038/s41598-021-81464-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

R. Mendes ◽

J. C. B. da Silva ◽

J. M. Magalhaes ◽

B. St-Denis ◽

D. Bourgault ◽

...

Keyword(s):

Numerical Modeling ◽

Internal Waves ◽

Coastal Waters ◽

Initial Conditions ◽

Spatial Scales ◽

River Plumes ◽

Wide Range ◽

Near Shore ◽

Generation Mechanisms ◽

Douro River

AbstractInternal waves (IWs) in the ocean span across a wide range of time and spatial scales and are now acknowledged as important sources of turbulence and mixing, with the largest observations having 200 m in amplitude and vertical velocities close to 0.5 m s−1. Their origin is mostly tidal, but an increasing number of non-tidal generation mechanisms have also been observed. For instance, river plumes provide horizontally propagating density fronts, which were observed to generate IWs when transitioning from supercritical to subcritical flow. In this study, satellite imagery and autonomous underwater measurements are combined with numerical modeling to investigate IW generation from an initial subcritical density front originating at the Douro River plume (western Iberian coast). These unprecedented results may have important implications in near-shore dynamics since that suggest that rivers of moderate flow may play an important role in IW generation between fresh riverine and coastal waters.

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