Biology subjects

Flotho, P.

Publications and source records attributed to Flotho, P..

4 recordsLinked to original sources

bioRxiv2025

ROSMAP-Compass: A data-harmonised, AI-ready atlas of 22 million single nuclei from the ROSMAP cohort

The Religious Orders Study and Memory and Aging Project (ROSMAP) cohort has generated the worlds most comprehensive single-cell transcriptomic resource for Alzheimers disease research. Naturally, in a project spanning multiple years with dozens of research groups involved, the resulting data landscape shows fragmentation across sequencing chemistries, protocols, and pipelines. This presents both a challenge and a unique opportunity for harmonized, collaborative analysis. Following an early data integration strategy and complete realignment of all single nucleus RNA sequencing data, we generated a fully harmonized resource: ROSMAP-Compass, comprising more than 22 million high-quality nuclei from 2,058 donors in multiple brain regions from the ROSMAP and Neuro Psychiatric Symptoms (NPS-AD) cohorts. Through systematic curation and unified reprocessing, we addressed substantial technical challenges including chemistry-specific biases, cross-study batch effects, and sample redundancies across multiple studies spanning different time periods and research groups. ROSMAP-Compass demonstrates the critical importance of systematic data harmonization when integrating large-scale single-cell datasets from multiple sources. By combining open science principles with cutting-edge AI integration, we provide both a critical resource for understanding Alzheimers disease heterogeneity and a blueprint for making complex biomedical data accessible to the global research community. The full resource, interactive web portal, and LLM compatible API are freely available, empowering researchers worldwide to accelerate discovery in neurodegenerative diseases.

neuroscience↗

bioRxiv2021

Software for Non-Parametric Image Registration of 2-Photon Imaging Data

Functional 2-photon microscopy is a key technology for imaging neuronal activity. The recorded image sequences, however, can contain non-rigid movement artifacts which requires high-accuracy movement correction. Variational optical flow (OF) estimation is a group of methods for motion analysis with established performance in many computer vision areas. However, it has yet to be adapted to the statistics of 2-photon neuroimaging data. In this work, we present the motion compensation method Flow-Registration that outperforms previous alignment tools and allows to align and reconstruct even low signal-to-noise ratio 2-photon imaging data and is able to compensate high-divergence displacements during local drug injections. The method is based on statistics of such data and integrates previous advances in variational OF estimation. Our method is available as an easy-to-use ImageJ / FIJI plugin as well as a MATLAB toolbox with modular, object oriented file IO, native multi-channel support and compatibility with existing 2-photon imaging suites.

neuroscience↗

bioRxiv2020

Fast Variational Alignment of non-flat 1D Displacements for Applications in Neuroimaging

BackgroundIn the context of signal analysis and pattern matching, alignment of 1D signals for the comparison of signal morphologies is an important problem. For image processing and computer vision, 2D optical flow (OF) methods find wide application for motion analysis and image registration and variational OF methods have been continuously improved over the past decades. New MethodWe propose a variational method for the alignment and displacement estimation of 1D signals. We pose the estimation of non-flat displacements as an optimization problem with a similarity and smoothness term similar to variational OF estimation. To this end, we can make use of efficient optimization strategies that allow real-time applications on consumer grade hardware. ResultsWe apply our method to two applications from functional neuroimaging: The alignment of 2-photon imaging line scan recordings and the denoising of evoked and event-related potentials in single trial matrices. We can report state of the art results in terms of alignment quality and computing speeds. Existing MethodsExisting methods for 1D alignment target mostly constant displacements, do not allow native subsample precision or precise control over regularization or are slower than the proposed method. ConclusionsOur method is implemented as a MATLAB toolbox and is online available. It is suitable for 1D alignment problems, where high accuracy and high speed is needed and non-constant displacements occur.

neuroscience↗

bioRxiv2019

Vestigial Auriculomotor Activity Indicates the Direction of Auditory Attention in Humans

It is commonly assumed that, unlike dogs and cats, we humans do not make ear movements when focusing our attention reflexively toward novel sounds or voluntarily toward those that are goal-relevant. In fact, it has been suggested that we do have a pinna-orienting system. Although this system became vestigial about 25 million years ago, it still exists as a \"neural fossil\" within the brain. Consistent with this hypothesis, we demonstrate for the first time that the direction of auditory attention is reflected in the sustained electrical activity of muscles within the vestigial auriculomotor system.\n\nSurface electromyograms (EMGs) were taken from muscles that either move the pinna or alter its shape. To assess reflexive, stimulus-driven attention we presented novel sounds from speakers at four different lateral locations while the participants silently read a boring text in front of them. To test voluntary, goal-directed attention we instructed participants to listen to a short story coming from one of these speakers, while ignoring a competing story from the corresponding speaker on the opposite side.\n\nIn both experiments, EMG recordings showed larger activity at the ear on the side of the attended stimulus, but with slightly different patterns. Upward movement (perking) differed according to the lateral focus of attention only during voluntary orienting; rearward folding of the pinnas upper-lateral edge exhibited such differences only during reflexive orienting. The existence of a pinna-orienting system in humans, one that is experimentally accessible, offers opportunities for basic as well as applied science. It could lead to a better understanding of the evolution of auditory attention and support the near real-time decoding of auditory attention in technical applications, for example, for attentionally controlled hearing aids that preferentially amplify sounds the user is attempting to listen to.

neuroscience↗