Daniela Ushizima
YOU?
Author Swipe
View article: Unveiling the distinct roles of <i>p</i> ‐tau, iron and MAOB in neurobiological basis of F18‐flortaucipir signal with voxel‐to‐voxel histology to PET analysis in different tauopathies
Unveiling the distinct roles of <i>p</i> ‐tau, iron and MAOB in neurobiological basis of F18‐flortaucipir signal with voxel‐to‐voxel histology to PET analysis in different tauopathies Open
Background Flortaucipir F 18 was the first FDA approved PET tracer to detect tau pathology. Previous studies show that Flortaucipir is sensitive to Alzheimer’s disease tau but not four‐repeat tauopathies. Furthermore, the neurobiological b…
View article: Breaking the reproducibility barrier with standardized protocols for plant-microbiome research.
Breaking the reproducibility barrier with standardized protocols for plant-microbiome research. Open
Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems…
View article: Breaking the reproducibility barrier with standardized protocols for plant–microbiome research
Breaking the reproducibility barrier with standardized protocols for plant–microbiome research Open
Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems…
View article: Synthetic Scientific Image Generation with VAE, GAN, and Diffusion Model Architectures
Synthetic Scientific Image Generation with VAE, GAN, and Diffusion Model Architectures Open
Generative AI (genAI) has emerged as a powerful tool for synthesizing diverse and complex image data, offering new possibilities for scientific imaging applications. This review presents a comprehensive comparative analysis of leading gene…
View article: ASCRIBE-XR: Virtual Reality for Visualization of Scientific Imagery
ASCRIBE-XR: Virtual Reality for Visualization of Scientific Imagery Open
ASCRIBE-XR, a novel computational platform designed to facilitate the visualization and exploration of 3D volumetric data and mesh data in the context of synchrotron experiments, is described. Using Godot and PC-VR technologies, the platfo…
View article: Foundation Models for Zero-Shot Segmentation of Scientific Images without AI-Ready Data
Foundation Models for Zero-Shot Segmentation of Scientific Images without AI-Ready Data Open
Zero-shot and prompt-based models have excelled at visual reasoning tasks by leveraging large-scale natural image corpora, but they often fail on sparse and domain-specific scientific image data. We introduce Zenesis, a no-code interactive…
View article: A machine-learning-driven data labeling pipeline for scientific analysis in <i>MLExchange</i>
A machine-learning-driven data labeling pipeline for scientific analysis in <i>MLExchange</i> Open
This study introduces a novel labeling pipeline to accelerate the labeling process of scientific data sets by using artificial intelligence (AI)-guided tagging techniques. This pipeline includes a set of interconnected web-based graphical …
View article: An Ensemble Approach for Brain Tumor Segmentation and Synthesis
An Ensemble Approach for Brain Tumor Segmentation and Synthesis Open
The integration of machine learning in magnetic resonance imaging (MRI), specifically in neuroimaging, is proving to be incredibly effective, leading to better diagnostic accuracy, accelerated image analysis, and data-driven insights, whic…
View article: Multi-laboratory Study Establishes Reproducible Methods for Plant-Microbiome Research in Fabricated Ecosystems
Multi-laboratory Study Establishes Reproducible Methods for Plant-Microbiome Research in Fabricated Ecosystems Open
Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems…
View article: Achieving the hydrogen shot: Interrogating ionomer interfaces
Achieving the hydrogen shot: Interrogating ionomer interfaces Open
The aim of this study is to enable the hydrogen economy and decarbonize various sectors in our environment that requires less expensive and more durable water electrolyzers, which can meet the Hydrogen-Shot target. The key is to improve th…
View article: batteryNET v0.0.1
batteryNET v0.0.1 Open
Code to organize, prepare, and segment multi-scan, larger-than-memory, volumetric dataset. Deep learning segmentation uses pytorch-lightning for code organization, logging and metrics, and multi-GPU parallelization of training and predicti…
View article: RhizoNet: semantic segmentation of plant roots using CNN (RhizoNet) v0.0.1
RhizoNet: semantic segmentation of plant roots using CNN (RhizoNet) v0.0.1 Open
RhizoNet is designed for the semantic segmentation of plant root scans, utilizing a sophisticated deep learning network known as Residual Unet. It specializes in processing color images of plants cultivated in a hydroponic EcoFAB system, c…
View article: Benchmarking topic models on scientific articles using BERTeley
Benchmarking topic models on scientific articles using BERTeley Open
The introduction of BERTopic marked a crucial advancement in topic modeling and presented a topic model that outperformed both traditional and modern topic models in terms of topic modeling metrics on a variety of corpora. However, unique …
View article: Deciphering the role of p‐tau, iron and MAOB in neurobiological basis of F18‐flortaucipir signal with voxel‐to‐voxel histology to PET analysis in different tauopathies
Deciphering the role of p‐tau, iron and MAOB in neurobiological basis of F18‐flortaucipir signal with voxel‐to‐voxel histology to PET analysis in different tauopathies Open
Background Flortaucipir F18 was the first FDA approved PET tracer to detect tau pathology. Previous studies show that Flortaucipir is more sensitive to Alzheimer’s disease (AD) tau than four‐repeat tauopathies. Furthermore, the neurobiolog…
View article: Deciphering the role of p‐tau, iron and MAOB in neurobiological basis of F18‐flortaucipir signal with voxel‐to‐voxel histology to PET analysis in different tauopathies
Deciphering the role of p‐tau, iron and MAOB in neurobiological basis of F18‐flortaucipir signal with voxel‐to‐voxel histology to PET analysis in different tauopathies Open
Background Flortaucipir F 18 was the first FDA approved PET tracer to detect tau pathology. Previous studies show that Flortaucipir is more sensitive to Alzheimer’s disease (AD) tau than four‐repeat tauopathies. Furthermore, the neurobiolo…
View article: Rhizonet: Image Segmentation for Plant Root in Hydroponic Ecosystem
Rhizonet: Image Segmentation for Plant Root in Hydroponic Ecosystem Open
Digital cameras have the ability to capture daily images of plant roots, allowing for the estimation of root biomass. However, the complexities of root structures and noisy image backgrounds pose challenges for advanced phenotyping. Manual…
View article: Lithium Metal Battery Quality Control via Transformer–CNN Segmentation
Lithium Metal Battery Quality Control via Transformer–CNN Segmentation Open
Lithium metal battery (LMB) has the potential to be the next-generation battery system because of its high theoretical energy density. However, defects known as dendrites are formed by heterogeneous lithium (Li) plating, which hinders the …
View article: Lithium Metal Battery Quality Control via Transformer-CNN Segmentation
Lithium Metal Battery Quality Control via Transformer-CNN Segmentation Open
Lithium metal battery (LMB) has the potential to be the next-generation battery system because of its high theoretical energy density. However, defects known as dendrites are formed by heterogeneous lithium (Li) plating, which hinders the …
View article: Deploying machine learning based segmentation for scientific imaging analysis at synchrotron facilities
Deploying machine learning based segmentation for scientific imaging analysis at synchrotron facilities Open
Scientific user facilities present a unique set of challenges for image processing due to the large volume of data generated from experiments and simulations. Furthermore, developing and implementing algorithms for real-time processing and…
View article: BERTeley v0.0.1
BERTeley v0.0.1 Open
This python package allows for the grouping of scientific articles based on their content, and generates topic words based on the groups. Overall this program can take in a large collection of articles and create a profile of them, display…
View article: A Cytopathologist Eye Assistant for Cell Screening
A Cytopathologist Eye Assistant for Cell Screening Open
Screening of Pap smear images continues to depend upon cytopathologists’ manual scrutiny, and the results are highly influenced by professional experience, leading to varying degrees of cell classification inaccuracies. In order to improve…
View article: Validation of Deep Learning Segmentation of CT Images of Fiber-Reinforced Composites
Validation of Deep Learning Segmentation of CT Images of Fiber-Reinforced Composites Open
Micro-computed tomography (µCT) is a valuable tool for visualizing microstructures and damage in fiber-reinforced composites. However, the large sets of data generated by µCT present a barrier to extracting quantitative information. Deep l…
View article: Deep learning for Alzheimer's disease: Mapping large-scale histological tau protein for neuroimaging biomarker validation
Deep learning for Alzheimer's disease: Mapping large-scale histological tau protein for neuroimaging biomarker validation Open
Abnormal tau inclusions are hallmarks of Alzheimer's disease and predictors of clinical decline. Several tau PET tracers are available for neurodegenerative disease research, opening avenues for molecular diagnosis in vivo. However, few ha…
View article: The role of biomarkers in cell counting with U‐Net CNN
The role of biomarkers in cell counting with U‐Net CNN Open
Background Imaging methods that are non‐destructive preserve tissue integrity and lead to improved topography analysis for the study of neurodegenerative diseases like Alzheimer’s Disease (AD). Immunofluorescence (IF) staining methods faci…
View article: Cultural Analytics of Large Datasets from Flickr
Cultural Analytics of Large Datasets from Flickr Open
Deluge became a metaphor to describe the amount of information to which we are subjected, and very often we feel we are drowning while our access to information is rising. Devising mechanisms for exploring massive image sets according to p…