Biology subjects

Villafane-Delgado, M.

Publications and source records attributed to Villafane-Delgado, M..

4 recordsLinked to original sources

bioRxiv2023

A Novel Semi-automated Proofreading and Mesh Error Detection Pipeline for Neuron Extension

AO_SCPLOWBSTRACTC_SCPLOWThe immense scale and complexity of neuronal electron microscopy (EM) datasets pose significant challenges in data processing, validation, and interpretation, necessitating the development of efficient, automated, and scalable error-detection methodologies. This paper proposes a novel approach that employs mesh processing techniques to identify potential error locations near neuronal tips. Error detection at tips is a particularly important challenge since these errors usually indicate that many synapses are falsely split from their parent neuron, injuring the integrity of the connectomic reconstruction. Additionally, we draw implications and results from an implementation of this error detection in a semi-automated proofreading pipeline. Manual proofreading is a laborious, costly, and currently necessary method for identifying the errors in the machine learning based segmentation of neural tissue. This approach streamlines the process of proofreading by systematically highlighting areas likely to contain inaccuracies and guiding proofreaders towards potential continuations, accelerating the rate at which errors are corrected.

neuroscience↗

bioRxiv2022

NeuVue: A Framework and Workflows for High-Throughput Electron Microscopy Connectomics Proofreading

Connectomic reconstruction from large image volumes produces segmentation and synaptic-assignment errors that must be resolved to support downstream analyses. As datasets have grown larger and teams more distributed, proofreading has become a critical operational bottleneck. Workflows for proofreading and error correction have not scaled commensurately with connectomic data production and may not accommodate heterogeneous proofreader expertise and machine-generated candidate edits. New tools are therefore needed to organize, prioritize, and coordinate proofreading at volume scale. Here we present NeuVue, a task-management and prioritization framework that operationalizes proofreading through atomic, auditable tasks for individual and team review, multistage routing across proofreader cohorts, performance and volume-state tracking, and integration with community annotation, visualization, and analysis services. We report the use of NeuVue across two volumetric datasets, supporting scalable proofreading by over forty proofreaders and producing over fifty thousand edits. NeuVue provides a reproducible human-in-the-loop framework for generating, validating, and maintaining large connectomic datasets.

neuroscience↗

bioRxiv2017

Neural Coding of Noisy and Reverberant Speech in Human Auditory Cortex

Speech communication in daily listening environments is complicated by the phenomenon of reverberation, wherein any sound reaching the ear is a mixture of the direct component from the source and multiple reflections off surrounding objects and the environment. The brain plays a central role in comprehending speech accompanied by such distortion, which, frequently, is further complicated by the presence of additional noise sources in the vicinity. Here, using magnetoencephalography (MEG) recordings from human subjects, we investigate the neural representation of speech in noisy, reverberant listening conditions as measured by phase-locked MEG responses to the slow temporal modulations of speech. Using systems-theoretic linear methods of stimulus encoding, we observe that the cortex maintains both distorted and distortion-free (cleaned) representations of speech. Also, we show that, while neural encoding of speech remains robust to additive noise in absence of reverberation, it is detrimentally affected by noise when present along with reverberation. Further, using linear methods of stimulus reconstruction, we show that theta-band neural responses are a likely candidate for the distortion free representation of speech, whereas delta band responses are more likely to carry non-speech specific information regarding the listening environment.

neuroscience↗

bioRxiv2017

Functional significance of spectrotemporal response functions obtained using magnetoencephalography

The spectrotemporal response function (STRF) model of neural encoding quantitatively associates dynamic auditory neural (output) responses to a spectrogram-like representation of a dynamic (input) stimulus. STRFs were experimentally obtained via whole-head human cortical responses to dynamic auditory stimuli using magnetoencephalography (MEG). The stimuli employed consisted of unpredictable pure tones presented at a range of rates. The predictive power of the estimated STRFs was found to be comparable to those obtained from the cortical single and multiunit activity literature. The STRFs were also qualitatively consistent with those obtained from electrophysiological studies in animal models; in particular their local-field-potential-generated spectral distributions and multiunit-activity-generated temporal distributions. Comparison of these MEG STRFs with others obtained using natural speech and music stimuli reveal a general structure consistent with common baseline auditory processing, including evidence for a transition in low-level neural representations of natural speech by 100 ms, when an appropriately chosen stimulus representation was used. It is also demonstrated that MEG-based STRFs contain information similar to that obtained using classic auditory evoked potential based approaches, but with extended applications to long-duration, non-repeated stimuli.\n\nAuthor summaryThe spectrotemporal response function (STRF) model of linking dynamic acoustic stimuli to dynamic neural responses is applied to whole-head non-invasive magnetoencephalography (MEG) recordings of the human auditory cortex. MEG STRFs were consistent predictors of neural activity, quantitatively and qualitatively, by comparison to those obtained from animal models using local field potential or multiunit activity as neural responses. Comparison of STRFs using stimuli as diverse as tone clouds, natural speech, and music revealed a common structure consistent with shared baseline auditory processing, when an appropriately chosen stimulus representation was used.

neuroscience↗