MATLAB in research projects

This topic is for instances of MATLAB being used in research, especially when it is specifically mentioned.

(Note: I am open for discussion on time frame of the research announcements. So far I have restricted myself to the last 6 months to keep it fresh, but opinions are welcome.)

[Star Strider]

I would keep the Nature and Science articles, regardless. Those journals are tightly edited, and while occasional research misconduct occurs, both journals quickly withdraw such papers when they are discovered. A ‘weak’ example is nevertheless an example. No software suite can do absolutely everything, at least not to date.

Intrigued by this thread, I did a PubMed search using only MATLAB as a search term. I retrieved 3569 citations.

[Walter Roberson]

In some of the cases it is clear that MATLAB was a key component. In other cases, it appears to be "What the researchers happened to have handy", mentioned mostly to satisfy submission guidelines.

Considering the number of items I have encountered already, for just 6 months and only two sources examined so far (and knowing I have not finished the second source), I am worrying about diluting the impact of the topic by including the ones where MATLAB relevance to the work seems weak.

If the item is one that excites about MATLAB being used in interesting ways, or if people are likely to want the MATLAB implementation of the project, then the item is worth posting.

If an item includes MATLAB code or says where the MATLAB code can be found, then I think it worth preserving. If MATLAB is clearly an important tool for the project, such as for the weather history time machine, or the terahertz filters, then the item is worth preserving. The "recoded organisms" one, though, gives the impression that something else could easily have been substituted for MATLAB.

I feel a bit more conflicted on cases such as the early drought detection. MATLAB is mentioned for the figures for that one. Does that imply an overall MATLAB implementation? Does it hint that the source code might be available? I would think it likely that other people would be interested in getting source for that project: it is an information analysis work. Whereas the recoded organisms paper is about lab techniques and biochemical pathways, and the source probably wouldn't be of much use to others.

[Steven Lord]

I'm not sure how tightly focused you'd like to keep this list, but the Beyond the Headlines blog on the MathWorks website lists how MathWorks products are used and have been used in stories that appear in journals, magazines, and generally in the news. Often the blog posts will link to journal articles about the work being discussed.

Answer 1

[Shlomo Geva]

I have used MATLAB since 1992. My first go-to platform. Every time. I am a tragic devotee. As a general computational platform I would not go as far suggesting that it is unique, but of course it has some unique features and capabilities. Simulink for instance is a fantastic tool and rather unique as far as general purpose visual Engineering simulation goes. However, despite all that, just like we no longer cite Isaac Newton or Gottfried Wilhelm Leibnitz every time we use calculus, we do not cite Matlab just because we use it. The use of Matlab if far more common than a search for the term "matlab" would indicate. Just like the term "calculus" would not indicate the true frequency of the use of calculus.

Answer 2

[Walter Roberson]

New filter could advance terahertz data transmission

"University of Utah engineers have discovered a new approach for designing filters capable of separating different frequencies in the terahertz spectrum. [...] Paulsen and Nahata discovered that by creating certain computer-generated designs using engineering software called MATLAB and printing them on a plastic sheet via a regular inkjet printer, they could create a filter that allows certain terahertz frequencies to pass through while blocking others out. The printer uses silver-metal ink similar to what is used for the production of circuit boards and tiny antennas."

Answer 3

[Walter Roberson]

Using 'fuzzy logic' to optimize hybrid solar/battery systems

"How did fuzzy logic help a group of researchers in Tunisia and Algeria create an ideal photovoltaic system that obeys the supply-and-demand principle and its delicate balance?

In the Journal of Renewable & Sustainable Energy, from AIP Publishing, the group describes a new sizing system of a solar array and a battery in a standalone photovoltaic system that is based on fuzzy logic -- a many-valued logic system designed to reason outputs by considering a range of possibilities rather than a simple, binary yes or no, as with classical logic. [...] "Our method applies Matlab/Simulink interfaces, which aren't complicated compared with other forms of simulation and model-based design," said Ben Salah. In fact, it's possible to build up a graphic integrated user interface to facilitate the usage of the proposed system. The group verified system performance with different inputs by simulations using calculated outputs."

Answer 4

[Walter Roberson]

Weather history 'time machine' created

"Building accurate computer reconstructions of historical global precipitation is tricky business. The statistical models are very complicated, the historical data is often full of holes, and researchers invariably have to make educated guesses at correcting for sampling errors.

The high degree of difficulty and expertise required means that relatively few climate scientists have been able to base their research on accurate models of historical precipitation. Now, a new software program developed by a research team including San Diego State University Distinguished Professor of Mathematics and Statistics Samuel Shen will democratize this ability, allowing far more researchers access to these models. [...] SOGP 1.0, which stands for a statistical technique known as spectral optimal gridding of precipitation, is based on the MATLAB programming language, commonly used in science and engineering. It reconstructs precipitation records for the entire globe (excluding the Polar Regions) between the years 1900 and 2011 and allows researchers to zoom in on particular regions and timeframes."

Answer 5

[Walter Roberson]

3D computational reconstruction of tissues with hollow spherical morphologies using single-cell gene expression data

"Single-cell gene expression analysis has contributed to a better understanding of the transcriptional heterogeneity in a variety of model systems, including those used in research in developmental, cancer and stem cell biology. Nowadays, technological advances facilitate the generation of large gene expression data sets in high-throughput format. Strategies are needed to pertinently visualize this information in a tissue structure–related context, so as to improve data analysis and aid the drawing of meaningful conclusions. Here we describe an approach that uses spatial properties of the tissue source to enable the reconstruction of hollow sphere–shaped tissues and organs from single-cell gene expression data in 3D space. To demonstrate our method, we used cells of the mouse otocyst and the renal vesicle as examples. This protocol presents a straightforward computational expression analysis workflow, and it is implemented on the MATLAB and R statistical computing and graphics software platforms. Hands-on time for typical experiments can be <1 h using a standard desktop PC or Mac."

Answer 6

[Walter Roberson]

Vibrational spectroscopic image analysis of biological material using multivariate curve resolution–alternating least squares (MCR-ALS)

"Raman and Fourier transform IR (FTIR) microspectroscopic images of biological material (tissue sections) contain detailed information about their chemical composition. The challenge lies in identifying changes in chemical composition, as well as locating and assigning these changes to different conditions (pathology, anatomy, environmental or genetic factors). Multivariate data analysis techniques are ideal for decrypting such information from the data. This protocol provides a user-friendly pipeline and graphical user interface (GUI) for data pre-processing and unmixing of pixel spectra into their contributing pure components by multivariate curve resolution–alternating least squares (MCR-ALS) analysis. The analysis considers the full spectral profile in order to identify the chemical compounds and to visualize their distribution across the sample to categorize chemically distinct areas. Results are rapidly achieved (usually <30–60 min per image), and they are easy to interpret and evaluate both in terms of chemistry and biology, making the method generally more powerful than principal component analysis (PCA) or heat maps of single-band intensities. In addition, chemical and biological evaluation of the results by means of reference matching and segmentation maps (based on k-means clustering) is possible."

(Table 2 makes obvious the MATLAB implementation)

Answer 7

[Walter Roberson]

Using mammalian GFP reconstitution across synaptic partners (mGRASP) to map synaptic connectivity in the mouse brain

"Many types of questions in neuroscience require the detection and mapping of synapses in the complex mammalian brain. A tool, mammalian GFP reconstitution across synaptic partners (mGRASP), offers a relatively easy, quick and economical approach to this technically challenging task. Here we describe in step-by-step detail the protocols for virus production, gene delivery, brain specimen preparation, fluorescence imaging and image analysis, calibrated substantially and specifically to make mGRASP-assisted circuit mapping (mGRASPing) practical in the mouse brain. The protocol includes troubleshooting suggestions and solutions to common problems. The mGRASP method is suitable for mapping mammalian synaptic connectivity at multiple scales: microscale for synapse-by-synapse or neuron-by-neuron analysis, and mesoscale for revealing local and long-range circuits. The entire protocol takes 5–6 weeks, including time for incubation and virus expression."

MATLAB implementation mentioned in Figure 4

[Walter Roberson]

Weak example? Should this one be kept?

Answer 8

[Walter Roberson]

A Vantage from Space Can Detect Earlier Drought Onset: An Approach Using Relative Humidity

"Each year, droughts cause significant economic and agricultural losses across the world. The early warning and onset detection of drought is of particular importance for effective agriculture and water resource management. Previous studies show that the Standard Precipitation Index (SPI), a measure of precipitation deficit, detects drought onset earlier than other indicators. Here we show that satellite-based near surface air relative humidity data can further improve drought onset detection and early warning. This paper introduces the Standardized Relative Humidity Index (SRHI) based on the NASA Atmospheric Infrared Sounder (AIRS) observations. The results indicate that the SRHI typically detects the drought onset earlier than the SPI. While the AIRS mission was not originally designed for drought monitoring, we show that its relative humidity data offers a new and unique avenue for drought monitoring and early warning. We conclude that the early warning aspects of SRHI may have merit for integration into current drought monitoring systems."

Figures are indicated as generated in MATLAB

[Walter Roberson]

Weak example? Should this one be kept?

Answer 9

[Walter Roberson]

Preliminary identification of palaeofloods with the alkane ratio C31/C17 and their potential link to global climate changes

"A major challenge in palaeohydrology is the extraction of continuous palaeoflood information from geophysical records. A high-resolution sediment core off the Minjiang estuary area in the Taiwan Strait, SE China, records the sedimentation history from approximately 1660 to the present. The alkane ratio C31/C17, a classic organic geochemical indicator of terrestrial/aquatic matter, peaks in the layers dating as 1876-1878 and 1968-1970, suggesting the large terrestrial input to the Minjiang estuary area by huge flood transporting during the each peak interval. Historical archives are consistent with this interpretations and record catastrophic floods in the Minjiang River during both intervals. Furthermore between 1876-1878 there were floods in southern China and droughts in northern China, as well as throughout Asia, Africa, Australia, and the Americas. The 1876-1878 catastrophic flood of the Minjiang River may therefore has been the local response to global climate anomalies during that time interval."

Map is indicated as created in MATLAB

[Walter Roberson]

Weak example? Should this one be kept?

Answer 10

[Walter Roberson]

Multi-channel EEG recordings during 3,936 grasp and lift trials with varying weight and friction

"WAY-EEG-GAL is a dataset designed to allow critical tests of techniques to decode sensation, intention, and action from scalp EEG recordings in humans who perform a grasp-and-lift task. Twelve participants performed lifting series in which the object’s weight (165, 330, or 660 g), surface friction (sandpaper, suede, or silk surface), or both, were changed unpredictably between trials, thus enforcing changes in fingertip force coordination. In each of a total of 3,936 trials, the participant was cued to reach for the object, grasp it with the thumb and index finger, lift it and hold it for a couple of seconds, put it back on the support surface, release it, and, lastly, to return the hand to a designated rest position. We recorded EEG (32 channels), EMG (five arm and hand muscles), the 3D position of both the hand and object, and force/torque at both contact plates. For each trial we provide 16 event times (e.g., ‘object lift-off’) and 18 measures that characterize the behaviour (e.g., ‘peak grip force’)."

Some MATLAB code is given.

Answer 11

[Walter Roberson]

An open science resource for establishing reliability and reproducibility in functional connectomics

"Efforts to identify meaningful functional imaging-based biomarkers are limited by the ability to reliably characterize inter-individual differences in human brain function. Although a growing number of connectomics-based measures are reported to have moderate to high test-retest reliability, the variability in data acquisition, experimental designs, and analytic methods precludes the ability to generalize results. The Consortium for Reliability and Reproducibility (CoRR) is working to address this challenge and establish test-retest reliability as a minimum standard for methods development in functional connectomics. Specifically, CoRR has aggregated 1,629 typical individuals’ resting state fMRI (rfMRI) data (5,093 rfMRI scans) from 18 international sites, and is openly sharing them via the International Data-sharing Neuroimaging Initiative (INDI). To allow researchers to generate various estimates of reliability and reproducibility, a variety of data acquisition procedures and experimental designs are included. Similarly, to enable users to assess the impact of commonly encountered artifacts (for example, motion) on characterizations of inter-individual variation, datasets of varying quality are included."

A number of different brain analysis tools are mentioned, including several based on MATLAB.

Answer 12

[Walter Roberson]

Quantitative multiplexing with nano-self-assemblies in SERS

"Multiplexed or simultaneous detection of multiple analytes is a valuable tool in many analytical applications. However, complications caused by the presence of interfering compounds in a sample form a major drawback in existing molecular sensor technologies, particularly in multi-analyte systems. Although separating analytes through extraction or chromatography can partially address the problem of interferents, there remains a need for developing direct observational tools capable of multiplexing that can be applied in situ. Surface-enhanced Raman Spectroscopy (SERS) is an optical molecular finger-printing technique that has the ability to resolve analytes from within mixtures. SERS has attracted much attention for its potential in multiplexed sensing but it has been limited in its quantitative abilities. Here, we report a facile supramolecular SERS-based method for quantitative multiplex analysis of small organic molecules in aqueous environments such as human urine."

Data analysis was carried out in MATLAB.

Answer 13

[Walter Roberson]

A model of face selection in viewing video stories

"When typical adults watch TV programs, they show surprisingly stereo-typed gaze behaviours, as indicated by the almost simultaneous shifts of their gazes from one face to another. However, a standard saliency model based on low-level physical features alone failed to explain such typical gaze behaviours. To find rules that explain the typical gaze behaviours, we examined temporo-spatial gaze patterns in adults while they viewed video clips with human characters that were played with or without sound, and in the forward or reverse direction. We here show the following: 1) the “peak” face scanpath, which followed the face that attracted the largest number of views but ignored other objects in the scene, still retained the key features of actual scanpaths, 2) gaze behaviours remained unchanged whether the sound was provided or not, 3) the gaze behaviours were sensitive to time reversal, and 4) nearly 60% of the variance of gaze behaviours was explained by the face saliency that was defined as a function of its size, novelty, head movements, and mouth movements. These results suggest that humans share a face-oriented network that integrates several visual features of multiple faces, and directs our eyes to the most salient face at each moment."

MATLAB was used for the analysis, including reference to a Caltech vision package based on MATLAB.

Answer 14

[Walter Roberson]

Combined effects of the Pacific Decadal Oscillation and El Niño-Southern Oscillation on Global Land Dry–Wet Changes

"The effects of natural variability, especially El Niño-Southern Oscillation (ENSO) effects, have been the focus of several recent studies on the change of drought patterns with climate change. The interannual relationship between ENSO and the global climate is not stationary and can be modulated by the Pacific Decadal Oscillation (PDO). However, the global land distribution of the dry–wet changes associated with the combination of ENSO and the PDO remains unclear. In the present study, this is investigated using a revised Palmer Drought Severity Index dataset (sc_PDSI_pm). We find that the effect of ENSO on dry–wet changes varies with the PDO phase. When in phase with the PDO, ENSO-induced dry–wet changes are magnified with respect to the canonical pattern. When out of phase, these dry–wet variations weaken or even disappear. This remarkable contrast in ENSO's influence between the two phases of the PDO highlights exciting new avenues for obtaining improved global climate predictions. In recent decades, the PDO has turned negative with more La Niña events, implying more rain and flooding over land. La Niña-induced wet areas become wetter and the dry areas become drier and smaller due to the effects of the cold PDO phase."

Maps and plots produced in MATLAB.

[Walter Roberson]

Weak example? Should this one be kept?

Answer 15

[Walter Roberson]

Nonstationary Precipitation Intensity-Duration-Frequency Curves for Infrastructure Design in a Changing Climate

"Extreme climatic events are growing more severe and frequent, calling into question how prepared our infrastructure is to deal with these changes. Current infrastructure design is primarily based on precipitation Intensity-Duration-Frequency (IDF) curves with the so-called stationary assumption, meaning extremes will not vary significantly over time. However, climate change is expected to alter climatic extremes, a concept termed nonstationarity. Here we show that given nonstationarity, current IDF curves can substantially underestimate precipitation extremes and thus, they may not be suitable for infrastructure design in a changing climate. We show that a stationary climate assumption may lead to underestimation of extreme precipitation by as much as 60%, which increases the flood risk and failure risk in infrastructure systems. We then present a generalized framework for estimating nonstationary IDF curves and their uncertainties using Bayesian inference. The methodology can potentially be integrated in future design concepts."

Figures created in MATLAB.

[Walter Roberson]

Weak example? Should this one be kept?

Answer 16

[Walter Roberson]

Neural antecedents of self-initiated actions in secondary motor cortex

"The neural origins of spontaneous or self-initiated actions are not well understood and their interpretation is controversial. To address these issues, we used a task in which rats decide when to abort waiting for a delayed tone. We recorded neurons in the secondary motor cortex (M2) and interpreted our findings in light of an integration-to-bound decision model. A first population of M2 neurons ramped to a constant threshold at rates proportional to waiting time, strongly resembling integrator output. A second population, which we propose provide input to the integrator, fired in sequences and showed trial-to-trial rate fluctuations correlated with waiting times. An integration model fit to these data also quantitatively predicted the observed inter-neuronal correlations. Together, these results reinforce the generality of the integration-to-bound model of decision-making. These models identify the initial intention to act as the moment of threshold crossing while explaining how antecedent subthreshold neural activity can influence an action without implying a decision."

Stepwise regression was done in MATLAB.

[Walter Roberson]

Weak example? Should this one be kept?

Answer 17

[Walter Roberson]

Recoded organisms engineered to depend on synthetic amino acids

"Here we describe the construction of a series of genomically recoded organisms (GROs)11 whose growth is restricted by the expression of multiple essential genes that depend on exogenously supplied synthetic amino acids (sAAs). "

Calculations via MATLAB

[Walter Roberson]

Weak example? Should this one be kept?

Answer 18

[Walter Roberson]

Synaptic molecular imaging in spared and deprived columns of mouse barrel cortex with array tomography

"A major question in neuroscience is how diverse subsets of synaptic connections in neural circuits are affected by experience dependent plasticity to form the basis for behavioral learning and memory. Differences in protein expression patterns at individual synapses could constitute a key to understanding both synaptic diversity and the effects of plasticity at different synapse populations. Our approach to this question leverages the immunohistochemical multiplexing capability of array tomography (ATomo) and the columnar organization of mouse barrel cortex to create a dataset comprising high resolution volumetric images of spared and deprived cortical whisker barrels stained for over a dozen synaptic molecules each. These dataset has been made available through the Open Connectome Project for interactive online viewing, and may also be downloaded for offline analysis using web, Matlab, and other interfaces."

MATLAB data access scripts are provided.

Answer 19

[Walter Roberson]

Novel Image Encryption based on Quantum Walks

"Quantum computation has achieved a tremendous success during the last decades. In this paper, we investigate the potential application of a famous quantum computation model, i.e., quantum walks (QW) in image encryption. It is found that QW can serve as an excellent key generator thanks to its inherent nonlinear chaotic dynamic behavior. Furthermore, we construct a novel QW-based image encryption algorithm. Simulations and performance comparisons show that the proposal is secure enough for image encryption and outperforms prior works. It also opens the door towards introducing quantum computation into image encryption and promotes the convergence between quantum computation and image processing."

Coding and timing tests were in MATLAB

[gege zhao]

Do you have source code？

[Walter Roberson]

Sorry, No.

Answer 20

[Walter Roberson]

Live cell imaging of membrane / cytoskeleton interactions and membrane topology

"We elucidate the interaction between actin and specific membrane components, using real time live cell imaging, by delivering probes that enable access to components, that cannot be accessed genetically. We initially investigated the close interplay between Phosphatidylinositol 4,5-bisphosphate (PIP2) and the F-actin network. We show that, during the early stage of cell adhesion, PIP2 forms domains within the filopodia membrane. We studied these domains alongside cell spreading and observed that these very closely follow the actin tread-milling. We show that this mechanism is associated with an active transport of PIP2 rich organelles from the cell perinuclear area to the edge, along actin fibers. Finally, mapping other phospholipids and membrane components we observed that the PIP2 domains formation is correlated with sphingosine and cholesterol rafts."

MATLAB code is provided in the PDF version.