Wavelet filtering before spike detection preserves waveform shape and enhances single-unit discrimination.
Ontology highlight
ABSTRACT:
SUBMITTER: Wiltschko AB
PROVIDER: S-EPMC2602872 | biostudies-literature | 2008 Aug
REPOSITORIES: biostudies-literature
Publications
Wavelet filtering before spike detection preserves waveform shape and enhances single-unit discrimination.
Wiltschko Alexander B AB Gage Gregory J GJ Berke Joshua D JD
Journal of neuroscience methods 20080528 1
The isolation of single units in extracellular recordings involves filtering. Removing lower frequencies allows a constant threshold to be applied in order to identify and extract action potential events. However, standard methods such as Butterworth bandpass filtering perform this frequency excision at a cost of grossly distorting waveform shapes. Here, we apply wavelet decomposition and reconstruction as a filter for electrophysiology data and demonstrate its ability to better preserve spike s ...[more]
Similar Datasets
Project description:BackgroundPubChem provides a 3-D neighboring relationship, which involves finding the maximal shape overlap between two static compound 3-D conformations, a computationally intensive step. It is highly desirable to avoid this overlap computation, especially if it can be determined with certainty that a conformer pair cannot meet the criteria to be a 3-D neighbor. As such, PubChem employs a series of pre-filters, based on the concept of volume, to remove approximately 65% of all conformer neighbor pairs prior to shape overlap optimization. Given that molecular volume, a somewhat vague concept, is rather effective, it leads one to wonder: can the existing PubChem 3-D neighboring relationship, which consists of billions of shape similar conformer pairs from tens of millions of unique small molecules, be used to identify additional shape descriptor relationships? Or, put more specifically, can one place an upper bound on shape similarity using other "fuzzy" shape-like concepts like length, width, and height?ResultsUsing a basis set of 4.18 billion 3-D neighbor pairs identified from single conformer per compound neighboring of 17.1 million molecules, shape descriptors were computed for all conformers. These steric shape descriptors included several forms of molecular volume and shape quadrupoles, which essentially embody the length, width, and height of a conformer. For a given 3-D neighbor conformer pair, the volume and each quadrupole component (Qx, Qy, and Qz) were binned and their frequency of occurrence was examined. Per molecular volume type, this effectively produced three different maps, one per quadrupole component (Qx, Qy, and Qz), of allowed values for the similarity metric, shape Tanimoto (ST) ? 0.8.The efficiency of these relationships (in terms of true positive, true negative, false positive and false negative) as a function of ST threshold was determined in a test run of 13.2 billion conformer pairs not previously considered by the 3-D neighbor set. At an ST ? 0.8, a filtering efficiency of 40.4% of true negatives was achieved with only 32 false negatives out of 24 million true positives, when applying the separate Qx, Qy, and Qz maps in a series (Qxyz). This efficiency increased linearly as a function of ST threshold in the range 0.8-0.99. The Qx filter was consistently the most efficient followed by Qy and then by Qz. Use of a monopole volume showed the best overall performance, followed by the self-overlap volume and then by the analytic volume.Application of the monopole-based Qxyz filter in a "real world" test of 3-D neighboring of 4,218 chemicals of biomedical interest against 26.1 million molecules in PubChem reduced the total CPU cost of neighboring by between 24-38% and, if used as the initial filter, removed from consideration 48.3% of all conformer pairs at almost negligible computational overhead.ConclusionBasic shape descriptors, such as those embodied by size, length, width, and height, can be highly effective in identifying shape incompatible compound conformer pairs. When performing a 3-D search using a shape similarity cut-off, computation can be avoided by identifying conformer pairs that cannot meet the result criteria. Applying this methodology as a filter for PubChem 3-D neighboring computation, an improvement of 31% was realized, increasing the average conformer pair throughput from 154,000 to 202,000 per second per CPU core.
| S-EPMC3158422 | biostudies-literature
Project description:Traditionally, the key step before decoding motor intentions from cortical recordings is spike sorting, the process of identifying which neuron was responsible for an action potential. Recently, researchers have started investigating approaches to decoding which omit the spike sorting step, by directly using information about action potentials' waveform shapes in the decoder, though this approach is not yet widespread. Particularly, one recent approach involves computing the moments of waveform features and using these moment values as inputs to decoders. This computationally inexpensive approach was shown to be comparable in accuracy to traditional spike sorting. In this study, we use offline data recorded from two Rhesus monkeys to further validate this approach. We also modify this approach by using sums of exponentiated features of spikes, rather than moments. Our results show that using waveform feature sums facilitates significantly higher hand movement reconstruction accuracy than using waveform feature moments, though the magnitudes of differences are small. We find that using the sums of one simple feature, the spike amplitude, allows better offline decoding accuracy than traditional spike sorting by expert (correlation of 0.767, 0.785 vs. 0.744, 0.738, respectively, for two monkeys, average 16% reduction in mean-squared-error), as well as unsorted threshold crossings (0.746, 0.776; average 9% reduction in mean-squared-error). Our results suggest that the sums-of-features framework has potential as an alternative to both spike sorting and using unsorted threshold crossings, if developed further. Also, we present data comparing sorted vs. unsorted spike counts in terms of offline decoding accuracy. Traditional sorted spike counts do not include waveforms that do not match any template ("hash"), but threshold crossing counts do include this hash. On our data and in previous work, hash contributes to decoding accuracy. Thus, using the comparison between sorted spike counts and threshold crossing counts to evaluate the benefit of sorting is confounded by the presence of hash. We find that when the comparison is controlled for hash, performing sorting is better than not. These results offer a new perspective on the question of to sort or not to sort.
| S-EPMC5513987 | biostudies-literature
Project description:Wavelet transform (WT) is a commonly used method for noise suppression and feature extraction from biomedical images. The selection of WT system settings significantly affects the efficiency of denoising procedure. This comparative study analyzed the efficacy of the proposed WT system on real 292 ultrasound images from several areas of interest. The study investigates the performance of the system for different scaling functions of two basic wavelet bases, Daubechies and Symlets, and their efficiency on images artificially corrupted by three kinds of noise. To evaluate our extensive analysis, we used objective metrics, namely structural similarity index (SSIM), correlation coefficient, mean squared error (MSE), peak signal-to-noise ratio (PSNR) and universal image quality index (Q-index). Moreover, this study includes clinical insights on selected filtration outcomes provided by clinical experts. The results show that the efficiency of the filtration strongly depends on the specific wavelet system setting, type of ultrasound data, and the noise present. The findings presented may provide a useful guideline for researchers, software developers, and clinical professionals to obtain high quality images.
| S-EPMC9262246 | biostudies-literature
Project description:Background and Objective: The emergence of the nonnutritive suck (NNS) pattern in preterm infants reflects the integrity of the brain and is used by clinicians in the neonatal intensive care unit (NICU) to assess feeding readiness and oromotor development. A critical need exists for an integrated software platform that provides NNS signal preprocessing, adaptive waveform discrimination, feature detection, and batch processing of big data sets across multiple NICU sites. Thus, the goal was to develop and describe a cross-platform graphical user interface (GUI) and terminal application known as NeoNNS for single and batch file time series and frequency-domain analyses of NNS compression pressure waveforms using analysis parameters derived from previous research on NNS dynamics. Methods. NeoNNS was implemented with Python and the Tkinter GUI package. The NNS signal-processing pipeline included a low-pass filter, asymmetric regression baseline correction, NNS peak detection, and NNS burst classification. Data visualizations and parametric analyses included time- and frequency-domain view, NNS spatiotemporal index view, and feature cluster analysis to model oral feeding readiness. Results. 568 suck assessment files sampled from 30 extremely preterm infants were processed in the batch mode (<50 minutes) to generate time- and frequency-domain analyses of infant NNS pressure waveform data. NNS cycle discrimination and NNS burst classification yield quantification of NNS waveform features as a function of postmenstrual age. Hierarchical cluster analysis (based on the Tsfresh python package and NeoNNS) revealed the capability to label NNS records for feeding readiness. Conclusions. NeoNNS provides a versatile software platform to rapidly quantify the dynamics of NNS development in time and frequency domains at cribside over repeated sessions for an individual baby or among large numbers of preterm infants at multiple hospital sites to support big data analytics. The hierarchical cluster feature analysis facilitates modeling of feeding readiness based on quantitative features of the NNS compression pressure waveform.
| S-EPMC6378788 | biostudies-literature
Project description:One of the main goals of shotgun proteomics studies is to identify by mass spectrometry as many proteins as possible, often from low-protein samples, in order to help answer important biological questions. All experimental steps need to be optimized to achieve a thorough proteomic analysis. One of the most important is an optimal extraction and solubilization of proteins through the use of detergents, chaotropes, and reducing agents. Although very efficient in solubilizing membrane proteins, the presence of these detergents, such as SDS, negatively affects the LC/MS analysis and limits protein identifications, and therefor they need to be removed before LC-MS analysis. Filter-aided sample preparation (FASP) is a generally accepted method for removal of detergents and chaotropes used for protein extraction as well as non-proteinaceous compounds such as salts, nucleic acids and lipids. Another critical aspect of proteomic analyses is the starting amount of protein in the sample. There is still little information about the efficacy of FASP method for protein-limited samples. The aim of this study was to compare two methods for SDS removal, ethanol precipitation versus FASP and we evaluate the effectiveness of FASP method using different filtration devices, as well as RIPA (0.1% SDS) and high-SDS (2%SDS) lysis buffers applied to low (1µg) and high (10-100µg) protein amounts.
2020-11-05 | PXD003400 | Pride
Project description:At many synapses in the central nervous system, spikes within high-frequency trains have a better chance of driving the postsynaptic neuron than spikes occurring in isolation. We asked what mechanism accounts for this selectivity at the retinogeniculate synapse. The amplitude of synaptic potentials was remarkably constant, ruling out a major role for presynaptic mechanisms such as synaptic facilitation. Instead, geniculate spike trains could be predicted from retinal spike trains on the basis of postsynaptic summation. This simple form of integration explains the response differences between a geniculate neuron and its main retinal driver, and thereby determines the flow of visual information to cortex.
| S-EPMC2901808 | biostudies-literature
Project description:BackgroundDuring cardiopulmonary resuscitation (CPR), there is a high incidence of capnograms distorted by chest compression artifact. This phenomenon adversely affects the reliability of automated ventilation detection based on the analysis of the capnography waveform. This study explored the feasibility of several filtering techniques for suppressing the artifact to improve the accuracy of ventilation detection.Materials and methodsWe gathered a database of 232 out-of-hospital cardiac arrest defibrillator recordings containing concurrent capnograms, compression depth and transthoracic impedance signals. Capnograms were classified as non-distorted or distorted by chest compression artifact. All chest compression and ventilation instances were also annotated. Three filtering techniques were explored: a fixed-coefficient (FC) filter, an open-loop (OL) adaptive filter, and a closed-loop (CL) adaptive filter. The improvement in ventilation detection was assessed by comparing the performance of a capnogram-based ventilation detection algorithm with original and filtered capnograms.ResultsSensitivity and positive predictive value of the ventilation algorithm improved from 91.9%/89.5% to 97.7%/96.5% (FC filter), 97.6%/96.7% (OL), and 97.0%/97.1% (CL) for the distorted capnograms (42% of the whole set). The highest improvement was obtained for the artifact named type III, for which performance improved from 77.8%/74.5% to values above 95.5%/94.5%. In addition, errors in the measurement of ventilation rate decreased and accuracy in the detection of over-ventilation increased with filtered capnograms.ConclusionsCapnogram-based ventilation detection during CPR was enhanced after suppressing the artifact caused by chest compressions. All filtering approaches performed similarly, so the simplicity of fixed-coefficient filters would take advantage for a practical implementation.
| S-EPMC6072040 | biostudies-literature
Project description:Filtering capacitor is a necessary component in the modern electronic circuit. Traditional filtering capacitor is often limited by its bulky and rigid configuration and narrow workable scope of applications. Here, an aqueous hybrid electrochemical capacitor is developed for alternating current line filtering with an applicable wide frequency range from 1 to 10,000 Hz. This capacitor possesses an areal specific energy density of 438 μF V2 cm-2 at 120 Hz, which to the best of our knowledge is record high among aqueous electrochemical capacitors reported so far. It can convert arbitrary alternating current waveforms and even noises to straight signals. After integration of capacitor units, a workable voltage up to hundreds of volts (e.g., 200 V) could be achieved without sacrificing its filtering capability. The integrated features of wide frequency range and high workable voltage for this capacitor present promise for multi-scenario and applicable filtering capacitors of practical importance.
| S-EPMC6598994 | biostudies-literature
Project description:Extracellular multi-unit recording is a widely used technique to study spontaneous and evoked neuronal activity in awake behaving animals. These recordings are done using either single-wire or multiwire electrodes such as tetrodes. In this study we have tested the ability of single-wire electrodes to discriminate activity from multiple neurons under conditions of varying noise and neuronal cell density. Using extracellular single-unit recording, coupled with iontophoresis to drive cell activity across a wide dynamic range, we studied spike waveform variability, and explored systematic differences in single-unit spike waveform within and between brain regions as well as the influence of signal-to-noise ratio (SNR) on the similarity of spike waveforms. We also modelled spike misclassification for a range of cell densities based on neuronal recordings obtained at different SNRs. Modelling predictions were confirmed by classifying spike waveforms from multiple cells with various SNRs using a leading commercial spike-sorting system. Our results show that for single-wire recordings, multiple units can only be reliably distinguished under conditions of high recording SNR (? 4) and low neuronal density (? 20,000/ mm(3)). Physiological and behavioural changes, as well as technical limitations typical of awake animal preparations, reduce the accuracy of single-channel spike classification, resulting in serious classification errors. For SNR <4, the probability of misclassifying spikes approaches 100% in many cases. Our results suggest that in studies where the SNR is low or neuronal density is high, separation of distinct units needs to be evaluated with great caution.
| S-EPMC3373584 | biostudies-literature
Project description:RNA SHAPE experiments have become important and successful sources of information for RNA structure prediction. In such experiments, chemical reagents are used to probe RNA backbone flexibility at the nucleotide level, which in turn provides information on base pairing and therefore secondary structure. Little is known, however, about the statistics of such SHAPE data. In this work, we explore different representations of noise in SHAPE data and propose a statistically sound framework for extracting reliable reactivity information from multiple SHAPE replicates. Our analyses of RNA SHAPE experiments underscore that a normal noise model is not adequate to represent their data. We propose instead a log-normal representation of noise and discuss its relevance. Under this assumption, we observe that processing simulated SHAPE data by directly averaging different replicates leads to bias. Such bias can be reduced by analyzing the data following a log transformation, either by log-averaging or Kalman filtering. Application of Kalman filtering has the additional advantage that a prior on the nucleotide reactivities can be introduced. We show that the performance of Kalman filtering is then directly dependent on the quality of that prior. We conclude the paper with guidelines on signal processing of RNA SHAPE data.
| S-EPMC6248965 | biostudies-literature