BacStalk: A comprehensive and interactive image analysis software tool for bacterial cell biology.

Prokaryotic cells display a striking subcellular organization. Studies of the underlying mechanisms in different species have greatly enhanced our understanding of the morphological and physiological adaptation of bacteria to different environmental niches. The image analysis software tool BacStalk is designed to extract comprehensive quantitative information from the images of morphologically complex bacteria with stalks, flagella, or other appendages. The resulting data can be visualized in interactive demographs, kymographs, cell lineage plots, and scatter plots to enable fast and thorough data analysis and representation. Notably, BacStalk can generate demographs and kymographs that display fluorescence signals within the two-dimensional cellular outlines, to accurately represent their subcellular location. Beyond organisms with visible appendages, BacStalk is also suitable for established, non-stalked model organisms with common or uncommon cell shapes. BacStalk, therefore, contributes to the advancement of prokaryotic cell biology and physiology, as it widens the spectrum of easily accessible model organisms and enables highly intuitive and interactive data analysis and visualization.

Evaluation of clinical value of videokymography for diagnosis and treatment of voice disorders.

This study aimed at determining the clinical value of videokymography (VKG) as an additional tool for the assessment of voice disorders. 105 subjects with voice disorders were examined by an experienced laryngologist. A questionnaire was used to specify diagnosis, diagnostic confidence, and treatment recommendations before and after VKG. The first part of questionnaire was filled by the laryngologist for each patient after routine ear-nose-throat evaluation, including stroboscopy, the second part after the subsequent VKG examination. In 31% of subjects VKG confirmed the stroboscopic diagnosis, in 44% it made the diagnosis more accurate, in 20% there was adjustment of the treatment, and in 5% it was not found diagnostically useful. After VKG the diagnostic confidence increased in 68% of the subjects. VKG may help clinicians to take some important treatment decisions and may be recommended to be performed in patients, where clinicians are uncertain about diagnosis and treatment.

Simple and direct assembly of kymographs from movies using KYMOMAKER.

In tracking analysis, the movement of cargos by motor proteins in axons is often represented by a time-space plot termed a 'kymograph'. Manual creation of kymographs is time-consuming and complicated for cell biologists. Therefore, we developed KYMOMAKER, a simple system that automatically creates a kymograph from a movie without generating multiple time-dissected movie stacks. In addition, KYMOMAKER can automatically extract faint vesicle traces, and can thereby effectively analyze cargos expressed at low levels in axons. A filter can be applied to remove traces of non-physiological movements and to extract meaningful traces of anterograde or retrograde cargo transport. For example, only cargos that move at a speed of >0.4 µm/second for a distance of >1 µm can be included. Another function of KYMOMAKER is to create a color kymograph in which the color of the trace varies according to the position of the fluorescent particle in the axis perpendicular to the long axis of the axon. Such positional information is completely lost in conventional kymographs. KYMOMAKER is an open access program that can be easily used to analyze vesicle transport in axons by cell biologists who do not have specific knowledge of bioimage informatics.

Quantifying Protein Dynamics by Kymograph Analysis.

Time-lapse imaging of the subcellular localization and dynamic behavior of proteins is critical to understand their biological functions in cells. With the advent of various methodologies and computational tools, the precise tracking and quantification of protein spatiotemporal dynamics have become feasible. Kymograph analysis, in particular, has been extensively adopted for the quantitative assessment of proteins, vesicles, and organelle movements. However, conventional kymograph analysis, which is based on a single linear trajectory, may not comprehensively capture the complexity of proteins that alter their course during intracellular transport and activity. In this chapter, we introduced an advanced protocol for whole-cell kymograph analysis that allows for three-dimensional (3D) tracking of protein dynamics. This method was validated through the analysis of tip-focused endocytosis and exocytosis processes in growing tobacco pollen tubes by employing both the advanced whole-cell and classical kymograph methods. In addition, we enhanced this method by integrating pseudo-colored kymographs that enables the direct visualization of changes in protein fluorescence intensity with fluorescence recovery after photobleaching to advance our understanding of protein localization and dynamics. This comprehensive method offers a novel insight into the intricate dynamics of protein activity within the cellular context.

A Hands-on Guide to AmoePy - a Python-Based Software Package to Analyze Cell Migration Data.

Amoeboid cell motility is fundamental for a multitude of biological processes such as embryogenesis, immune responses, wound healing, and cancer metastasis. It is characterized by specific cell shape changes: the extension and retraction of membrane protrusions, known as pseudopodia. A common approach to investigate the mechanisms underlying this type of cell motility is to study phenotypic differences in the locomotion of mutant cell lines. To characterize such differences, methods are required to quantify the contour dynamics of migrating cells. AmoePy is a Python-based software package that provides tools for cell segmentation, contour detection as well as analyzing and simulating contour dynamics. First, a digital representation of the cell contour as a chain of nodes is extracted from each frame of a time-lapse microscopy recording of a moving cell. Then, the dynamics of these nodes-referred to as virtual markers-are tracked as the cell contour evolves over time. From these data, various quantities can be calculated that characterize the contour dynamics, such as the displacement of the virtual markers or the local stretching rate of the marker chain. Their dynamics is typically visualized in space-time plots, the so-called kymographs, where the temporal evolution is displayed for the different locations along the cell contour. Using AmoePy, you can straightforwardly create kymograph plots and videos from stacks of experimental bright-field or fluorescent images of motile cells. A hands-on guide on how to install and use AmoePy is provided in this chapter.

Measuring Retrograde Actin Flow in Neuronal Growth Cones.

Actin flow refers to the motion of the F-actin cytoskeleton and has been observed in many different cell types, especially in motile cells including neuronal growth cones. The direction of the actin flow is generally retrograde from the periphery toward the center of the cell. Actin flow can be harnessed for forward movement of the cell through substrate-cytoskeletal coupling; thus, a key function of actin flow is in cell locomotion. In this chapter, we illustrate three different methods of quantifying retrograde F-actin flow in growth cones derived from cultured Aplysia bag cell neurons. These methods include tracking the movement of surface marker beads as well as kymograph analysis of time-lapse sequences acquired by differential interference contrast (DIC) imaging or fluorescent speckle microscopy (FSM). Due to their large size, Aplysia neuronal growth cones are uniquely suited for these methods; however, they can also be applied to any other growth cones with clear F-actin-rich peripheral domains.

Comparison between the acoustic fundamental frequency of the voice and the vibration frequency of the vocal folds analyzed by digital kymography. / Comparação entre a frequência fundamental acústica da voz e a frequência de vibração das pregas vocais analisada pela videoquimografia digital.

PURPOSE: To compare the frequency of vocal fold opening variation, analyzed by digital kymography, with the fundamental voice frequency obtained by acoustic analysis, in individuals without laryngeal alteration. METHODS: Observational analytical cross-sectional study. The participants were forty-eight women and 38 men from 18 to 55 years of age. The evaluation was made by voice acoustic analysis, by the habitual emission of the vowel /a/ for 3 seconds, and days of the week, and digital kymography (DKG), by the habitual emission of the vowels /i/ and /ɛ/. The measurements analyzed were acoustic fundamental frequency (f0), extracted by the Computerized Speech Lab (CSL) program, and dominant frequency of the variation of right (R-freq) and left (L-freq) vocal fold opening, obtained through the KIPS image processing program. The mounting of the kymograms consisted in the manual demarcation of the region by vertical lines delimiting width and horizontal lines separating the posterior, middle and anterior thirds of the Rima glottidis. In the statistical analysis, the Anderson-Darling test was used to verify the normality of the sample. The ANOVA and Tukey tests were performed for the comparison of measurements between the groups. For the comparison of age between the groups, the Mann-Whitney test was used. RESULTS: There are no differences between the values of the frequency measurement analyzed by digital kymography, with the acoustic fundamental frequency, in individuals without laryngeal alteration. CONCLUSION: The values of the dominant frequency of the vocal folds opening variation, as assessed by digital kymography, and the acoustic fundamental frequency of the voice are similar, allowing comparison between these measurements in the multidimensional evaluation of the voice, in individuals without laryngeal alteration.

OBJETIVO: Comparar a frequência da variação da abertura das pregas vocais, analisada pela videoquimografia digital, com a frequência fundamental da voz, obtida através da análise acústica, em indivíduos sem alteração laríngea. MÉTODO: Trata-se de um estudo observacional analítico transversal. Participaram 48 mulheres e 38 homens, de 18 a 55 anos. A avaliação foi composta por análise acústica da voz, obtida pela emissão habitual da vogal /a/ durante 3 segundos, e os dias da semana, e pela videoquimografia digital (DKG), obtida pela emissão habitual das vogais /i/ e /ɛ/. As medidas analisadas foram a frequência fundamental acústica (f0), extraída pelo programa Computerized Speech Lab (CSL), e a frequência dominante da variação de abertura da prega vocal direita (D-freq) e esquerda (E-freq), obtidas através do programa de processamento de imagens KIPS. A montagem dos quimogramas constou na demarcação manual da região, compostas por linhas verticais que delimitaram largura da prega vocal e linhas horizontais que marcaram os terços posterior, médio e anterior da rima glótica. Na análise estatística, o teste Anderson-Darling foi utilizado para verificar a normalidade da amostra. Os testes ANOVA e Tukey foram realizados para a comparação das medidas entre os grupos. Para a comparação da idade entre os grupos, foi utilizado o teste Mann-Whitney. RESULTADOS: Não existem diferenças entre os valores da medida de frequência analisada pela videoquimografia digital, com a frequência fundamental acústica, em indivíduos sem alteração laríngea. CONCLUSÃO: Os valores da frequência dominante da variação de abertura das pregas vocais, avaliada pela videoquimografia digital, e a frequência fundamental acústica da voz são similares, permitindo uma comparação entre estas medidas na avaliação multidimensional da voz, em indivíduos sem alteração laríngea.

Evaluation of Voice and Vocal Fold Vibration after Thyroidectomy Using Two-Dimensional Scanning Digital Kymography and High-Speed Videolaryngoscopy.

OBJECTIVE: Vocal dysfunction is one of the major factors that affect the health-related quality of life of patients after thyroidectomy. Conventionally, voice changes after thyroidectomy have been evaluated by videostroboscopy and acoustic analysis. Recently, two-dimensional scanning digital kymography (2D DKG) and high-speed videolaryngoscopy (HSV) have been developed and have shown usefulness in accurately evaluating vocal fold vibration. This study aimed to evaluate changes of vocal fold vibration and voice after thyroidectomy using 2D DKG and HSV. MATERIALS AND METHODS: We evaluated the voice and vocal fold movement of 24 female patients who underwent thyroidectomy in a single tertiary hospital from December 2018 to October 2019. We obtained serial 2D DKG and HSV data one day before thyroidectomy, and 1 week and 1 month after surgery. We analyzed the peak glottal area of HSV, amplitude symmetry index, phase symmetry index, and open quotient using the 2D DKG data. The parameters were calculated at three levels of the vocal fold (line 1=anterior, line 2=middle, line 3=posterior). In the same period, we performed a voice analysis evaluating voice frequency, jitter, shimmer, and noise to harmonic ratio. We also assessed maximum phonation time and subjective voice changes with voice handicap index-10 questionnaires. RESULTS: Highest frequency (F-high), frequency range (F-range), and fundamental frequency (F0) decreased at 1 week and 1 month after thyroidectomy compared with preoperative values (P = 0.003, 0.004, <0.001 and P = 0.002, 0.015, 0.001 at 1 week and 1 month, respectively). The open quotient of 2D DKG in lines 1 and 2 increased at 1 week after thyroidectomy (P = 0.011, 0.006) and recovered to preoperative levels at 1 month postoperatively (P = 0.189, 0.153). Other quantitative measures by 2D DKG and HSV did not show significant changes between the preoperative and postoperative periods. In a correlation analysis between vocal parameters from the acoustic analysis and the values obtained from 2D DKG and HSV, significant negative correlations were observed between peak glottal area and three factors (F-high, F-range, and F0) at 1 month after surgery (r = -0.589, -0.529, -0.708; P = 0.002, 0.008, <0.001, respectively). There were positive correlations between phase symmetry indexes in lines 1 and 2 and shimmer at 1 week after thyroidectomy (r = 0.489, 0.425; P = 0.015, 0.038, respectively). Phase symmetry index in line 3 showed a significant negative correlation with maximum phonation time at both 1 week and 1 month after surgery (r = -0.497, -0.439; P = 0.013, 0.032, respectively). However, there was no correlation between total score on the voice handicap index-10 questionnaires and quantitative measurements of vocal fold vibration. CONCLUSION: 2D DKG and HSV may provide important information on vocal fold vibratory patterns after thyroidectomy, and measurements made with them were correlated with maximal phonation time and acoustic parameters such as F-high, F-range, F0, shimmer.

A fast and robust method for automated analysis of axonal transport.

Cargo movement along axons and dendrites is indispensable for the survival and maintenance of neuronal networks. Key parameters of this transport such as particle velocities and pausing times are often studied using kymograph construction, which converts the transport along a line of interest from a time-lapse movie into a position versus time image. Here we present a method for the automatic analysis of such kymographs based on the Hough transform, which is a robust and fast technique to extract lines from images. The applicability of the method was tested on simulated kymograph images and real data from axonal transport of synaptophysin and tetanus toxin as well as the velocity analysis of synaptic vesicle sharing between adjacent synapses in hippocampal neurons. Efficiency analysis revealed that the algorithm is able to detect a wide range of velocities and can be used at low signal-to-noise ratios. The present work enables the quantification of axonal transport parameters with high throughput with no a priori assumptions and minimal human intervention.

Improved kymography tools and its applications to mitosis.

Although applicability of kymographs is limited to nearly one-dimensional (1D) processes, they have been instrumental in the analysis and interpretation of a wide range of dynamic biological processes. We focus here on some applications of kymography in the study of one among the range of 'nearly-1D' processes -mitosis. Using this biological context, we suggest generalized procedures in kymograph assembly that allow a partial retrieval of spatial information which is typically lost or distorted in conventional kymography. These kymograph variations, namely guided-kymography and chromo-kymography, are helpful in the determination of actual velocities and discrimination of structures when using thick regions of interest (ROIs). The method used to generate chromo-kymographs is generalized to other (non-kymograph) projection techniques, which include time-stack and z-stack projections.

Comparative analysis of high-speed videolaryngoscopy images and sound data simultaneously acquired from rigid and flexible laryngoscope: a pilot study.

High-Speed Videoendoscopy (HSV) is becoming a robust tool for the assessment of vocal fold vibration in laboratory investigation and clinical practice. We describe the first successful application of flexible High Speed Videoendoscopy with innovative laser light source conducted in clinical settings. The acquired image and simultaneously recorded audio data are compared to the results obtained by means of a rigid endoscope. We demonstrated that the HSV recordings with fiber-optic laryngoscope have enabled obtaining consistently bright, color images suitable for parametrization of vocal fold oscillation similarly as in the case of the HSV data obtained from a rigid laryngoscope. The comparison of period and amplitude perturbation parameters calculated on the basis of image and audio data acquired from flexible and rigid HSV recording objectively confirm that flexible High-Speed Videoendoscopy is a more suitable method for examination of natural phonation. The HSV-based measures generated from this kymographic analysis are arguably a superior representation of the vocal fold vibrations than the acoustic analysis because their quantification is independent of the vocal tract influences. This experimental study has several implications for further research in the field of HSV application in clinical assessment of glottal pathologies nature and its effect on vocal folds vibrations.

Axonal stress kinase activation and tau misbehavior induced by kinesin-1 transport defects.

Many neurodegenerative diseases exhibit axonal pathology, transport defects, and aberrant phosphorylation and aggregation of the microtubule binding protein tau. While mutant tau protein in frontotemporal dementia and parkinsonism linked to chromosome 17 (FTDP17) causes aberrant microtubule binding and assembly of tau into filaments, the pathways leading to tau-mediated neurotoxicity in Alzheimer's disease and other neurodegenerative disorders in which tau protein is not genetically modified remain unknown. To test the hypothesis that axonal transport defects alone can cause pathological abnormalities in tau protein and neurodegeneration in the absence of mutant tau or amyloid beta deposits, we induced transport defects by deletion of the kinesin light chain 1 (KLC1) subunit of the anterograde motor kinesin-1. We found that upon aging, early selective axonal transport defects in mice lacking the KLC1 protein (KLC1-/-) led to axonopathies with cytoskeletal disorganization and abnormal cargo accumulation. In addition, increased c-jun N-terminal stress kinase activation colocalized with aberrant tau in dystrophic axons. Surprisingly, swollen dystrophic axons exhibited abnormal tau hyperphosphorylation and accumulation. Thus, directly interfering with axonal transport is sufficient to activate stress kinase pathways initiating a biochemical cascade that drives normal tau protein into a pathological state found in a variety of neurodegenerative disorders including Alzheimer's disease.

Collagen injection for correcting vocal fold asymmetry: high-speed imaging.

OBJECTIVES: We hypothesized that high-speed digital imaging with videokymographic and laryngotopographic analysis would provide a quantitative method to evaluate the effect of collagen injection for the correction of asymmetric and irregular vocal fold vibration in unilateral vocal fold paralysis. METHODS: Videokymographic and laryngotopographic analysis was performed for high-speed digital recordings of vocal fold vibration for visualizing the glottal vibratory patterns, and for quantifying the frequency of vibration of each vocal fold, respectively, including comparisons between the paralyzed and normal vocal folds before and after surgery. This included prospective observations of 11 subjects with unilateral vocal fold paralysis (4 male, 7 female; mean +/- SD age, 67.1 +/- 12.0 years) using high-speed digital image analysis before and after collagen injection. RESULTS: Analysis of the laryngotopographs revealed 2 distinct frequencies of vibration for the paralyzed and contralateral vocal folds for 8 of the 11 subjects before surgery. After collagen injection, the vibration frequencies became identical, despite asymmetric vibration amplitudes. Asymmetric vibration amplitudes were also observed in the other 3 subjects before surgery, but the amplitudes became symmetric after collagen injection, despite a persistent phase shift. CONCLUSIONS: Asymmetric vibration in vocal fold paralysis was exemplified by differences in vibration frequency and amplitude between the vocal folds. The present study showed that after collagen injection, these aspects of vibratory patterns improved toward symmetry. This surgical procedure could improve the functional symmetry of the larynx for phonation.

Quantifying the polymerization dynamics of plant cortical microtubules using kymograph analysis.

The plant cortical microtubule array is a dynamic structure that confers cell shape and enables plants to alter their growth and development in response to internal and external cues. Cells use a variety of microtubule regulatory proteins to spatially and temporally modulate the intrinsic polymerization dynamics of cortical microtubules to arrange them into specific configurations and to reshape arrays to adapt to changing conditions. To obtain mechanistic insight into how particular microtubule regulatory proteins mediate the dynamic (re)structuring of cortical microtubule arrays, we need to measure their effect on the dynamics of cortical microtubules. In this chapter, we describe new ImageJ plugins to generate kymographs from time-lapse images and to analyze them to measure the parameters that quantitatively describe cortical microtubule dynamics.

Kymolyzer, a Semi-Autonomous Kymography Tool to Analyze Intracellular Motility.

The movement of intracellular cargo, such as transcripts, proteins, and organelles, is fundamental to cellular function. Neurons, due to their long axons and dendrites, are particularly dependent on proper intracellular trafficking and vulnerable to defects in the movement of intracellular cargo that are noted in neurodegenerative and neurodevelopmental disorders. Accurate quantification of intracellular transport is therefore needed for studying the mechanisms of cargo trafficking, the influence of mutations, and the effects of potentially therapeutic pharmaceuticals. In this article, we introduce an algorithm called "Kymolyzer." The algorithm can quantify intracellular trafficking along a defined path, such as that formed by the aligned microtubules of axons and dendrites. Kymolyzer works as a semi-autonomous kymography software application. It constructs and analyzes kymographs to measure the movement and distribution of fluorescently tagged objects along a user-defined path. The algorithm can be used under a wide variety of experimental conditions and can extract a diverse array of motility parameters describing intracellular movement, including time spent in motion, percentage of objects in motion, percentage of objects that are stationary, and velocities of motile objects. This article serves as a user manual describing the design of Kymolyzer, providing a stepwise protocol for its use and illustrating its functions with common examples. © 2020 Wiley Periodicals LLC Basic Protocol: Kymolyzer, a semi-autonomous kymography tool to analyze intracellular motility.

Analyzing Intracellular Gradients in Pollen Tubes.

Conspicuous intracellular gradients manifest and/or drive intracellular polarity in pollen tubes. However, quantifying these gradients raises multiple technical challenges. Here we present a sensible computational protocol to analyze gradients in growing pollen tubes and to filter nonrepresentative time points. As an example, we use imaging data from pollen tubes expressing a genetically encoded ratiometric Ca2+ probe, Yellow CaMeleon 3.6, from which a kymograph is extracted. The tip of the pollen tube is detected with CHUKNORRIS, our previously published methodology, allowing the reconstruction of the intracellular gradient through time. Statistically confounding time points, such as growth arrest where gradients are highly oscillatory, are filtered out and a mean spatial profile is estimated with a local polynomial regression method. Finally, we estimate the gradient slope by the linear portion of the decay in mean fluorescence, offering a quantitative method to detect phenotypes of gradient steepness, location, intensity, and variability. The data manipulation protocol proposed can be achieved in a simple and efficient manner using the statistical programming language R, opening paths to perform high-throughput spatiotemporal phenotyping of intracellular gradients in apically growing cells.

Determination of axonal transport velocities via image cross- and autocorrelation.

On their way to the synapse and back, neuronal proteins are carried in cargo vesicles along axons and dendrites. Here, we demonstrate that the key parameters of axonal transport, i.e., particle velocities and pausing times can be read out from CCD-camera images automatically. In the present study, this is achieved via cross- and autocorrelation of kymograph columns. The applicability of the method was measured on simulated kymographs and data from axonal transport timeseries of mRFP-labeled synaptophysin. In comparing outcomes of velocity determinations via a performance parameter that is analogous to the signal-to-noise ratio (SNR) definition, we find that outcomes are dependent on sampling, particle numbers and signal to noise of the kymograph. Autocorrelation of individual columns allows exact determination of pausing time populations. In contrast to manual tracking, correlation does not require experience, a priori assumptions or disentangling of individual particle trajectories and can operate at low SNR.

Depth-kymography of vocal fold vibrations: part II. Simulations and direct comparisons with 3D profile measurements.

We report novel direct quantitative comparisons between 3D profiling measurements and simulations of human vocal fold vibrations. Until now, in human vocal folds research, only imaging in a horizontal plane was possible. However, for the investigation of several diseases, depth information is needed, especially when the two folds act differently, e.g. in the case of tumour growth. Recently, with our novel depth-kymographic laryngoscope, we obtained calibrated data about the horizontal and vertical positions of the visible surface of the vibrating vocal folds. In order to find relations with physical parameters such as elasticity and damping constants, we numerically simulated the horizontal and vertical positions and movements of the human vocal folds while vibrating and investigated the effect of varying several parameters on the characteristics of the phonation: the masses and their dimensions, the respective forces and pressures, and the details of the vocal tract compartments. Direct one-to-one comparison with measured 3D positions presents-for the first time-a direct means of validation of these calculations. This may start a new field in vocal folds research.

KymoButler, a deep learning software for automated kymograph analysis.

Kymographs are graphical representations of spatial position over time, which are often used in biology to visualise the motion of fluorescent particles, molecules, vesicles, or organelles moving along a predictable path. Although in kymographs tracks of individual particles are qualitatively easily distinguished, their automated quantitative analysis is much more challenging. Kymographs often exhibit low signal-to-noise-ratios (SNRs), and available tools that automate their analysis usually require manual supervision. Here we developed KymoButler, a Deep Learning-based software to automatically track dynamic processes in kymographs. We demonstrate that KymoButler performs as well as expert manual data analysis on kymographs with complex particle trajectories from a variety of different biological systems. The software was packaged in a web-based 'one-click' application for use by the wider scientific community (http://kymobutler.deepmirror.ai). Our approach significantly speeds up data analysis, avoids unconscious bias, and represents another step towards the widespread adaptation of Machine Learning techniques in biological data analysis.

Many molecules and structures within cells have to move about to do their job. Studying these movements is important to understand many biological processes, including the development of the brain or the spread of viruses. Kymographs are images that represent the movement of particles in time and space. Unfortunately, tracing the lines that represent movement in kymographs of biological particles is hard to do automatically, so currently this analysis is done by hand. Manually annotating kymographs is tedious, time-consuming and prone to the researcher's unconscious bias. In an effort to simplify the analysis of kymographs, Jakobs et al. have developed KymoButler, a software tool that can do it automatically. KymoButler uses artificial intelligence to trace the lines in a kymograph and extract the information about particle movement. It speeds up analysis of kymographs by between 50 and 250 times, and comparisons show that it is as reliable as manual analysis. KymoButler is also significantly more effective than any previously existing automatic kymograph analysis programme. To make KymoButler accessible, Jakobs et al. have also created a website with a drag-and-drop facility that allows researchers to easily use the tool. KymoButler has been tested in many areas of biological research, from quantifying the movement of molecules in neurons to analysing the dynamics of the scaffolds that help cells keep their shape. This variety of applications showcases KymoButler's versatility, and its potential applications. Jakobs et al. are further contributing to the field of machine learning in biology with 'deepmirror.ai', an online hub with the goal of accelerating the adoption of artificial intelligence in biology.

Vibratory Characteristics of Diplophonia Studied by High Speed Video and Vibrogram Analysis.

Diplophonia can occur in patients with polyps, atrophy, paralysis, or scars. Its vibratory patterns have not been well characterized. High-speed video (HSV) analysis can contribute to their understanding. Twenty subjects with a diplophonic voice quality were studied by HSV. Diplophonia was due to medical causes including vocal fold paresis (n = 7), vocal atrophy (n = 5), polyps (n = 5), and scars/sulci (n = 3). The HSV was analyzed using a multislice digital videokymography (DKG). The DKG tracing was analyzed qualitatively and then transformed into a vibrogram waveform signal for frequency analysis. RESULTS: Vibratory abnormalities seen on HSVs explained the diplophonia. Subharmonics to the fundamental frequency can be visualized by DKG. None could be resolved by stroboscopy. One can stratify diplophonia as symmetric or asymmetric based on the involvement of one or both vocal folds. Scars and atrophy showed symmetric subharmonic production with ectopic beats every 4-10 beats. Some subjects showed anterior and posterior independent vocal fold oscillators. Asymmetric causes of diplophonia are common in patients with paralysis. Two different oscillation frequencies of each vocal fold generate in and then out of phase interaction between the two sides. Vibrogram analysis documents the frequent presence of interharmonic energy peaks above the dominant fundamental frequency. Eighteen of the 20 subjects have obvious subharmonic peaks. CONCLUSION: Patients with diplophonia have vibratory abnormalities arising from the vocal folds. HSV and vibrogram analysis followed by frequency analysis of the vibrogram can resolve vibratory abnormality into symmetric versus asymmetric causes and can document the type of vibratory abnormality.