25 papers · ranked by Valyu relevance
Robert R. Stickels, Evan Murray, Pawan Kumar, Jilong Li + 5 more
The precise spatial localization of molecular signals within tissues richly informs the mechanisms of tissue formation and function. Previously, we developed Slide-seq, a technology which enables transcriptome-wide measurements with 10-micron spatial resolution. Here, we report new modifications to Slide-seq library…
C.E. Brewster, F.G. Mann, B.W. Benham-Pyle, A. Sánchez Alvarado
Spatial transcriptomic techniques such as Slide-seqV2 uncover novel relationships and interactions between cell types by coupling gene expression and spatial data. Here we discuss two unexpected sources of error in Slide-seqV2 data, one physical and one computational. To address this we present an analysis pipeline…
Luli S. Zou, Tongtong Zhao, Dylan M. Cable, Evan Murray + 3 more
Allele-specific expression (ASE), or the preferential expression of one allele, can be observed in transcriptomics data from early development throughout the lifespan. However, the prevalence of spatial and cell type-specific ASE variation remains unclear. Spatial transcriptomics technologies permit the study of…
Jamie L. Marshall, Teia Noel, Qingbow S. Wang, Silvana Bazua-Valenti + 13 more
High resolution spatial transcriptomics is a transformative technology that enables mapping of RNA expression directly from intact tissue sections; however, its utility for the elucidation of disease processes and therapeutically actionable pathways remain largely unexplored. Here we applied Slide-seqV2 to mouse and…
Carolyn Brewster, Frederick G Mann Jr., Blair Benham-Pyle, Alejandro Sánchez Alvarado + 1 more
Spatial analysis of gene expression patterns has been a key technique for revealing the potential functions of genes. Traditionally, these analyses, conducted using in situ hybridizations and other labor-intensive protocols, were constrained to examining only a few candidate genes per sample. However, the advent of…
Wei Liu, Xu Liao, Ziye Luo, Yi Yang + 7 more
Spatially resolved transcriptomics are a set of emerging technologies that enable the transcriptomic profiling of tissues with the physical location of expressions. Although a variety of methods have been developed for data integration, most of them are for single-cell RNA-seq datasets without a consideration of…
Samuel G. Rodriques, Robert R. Stickels, Aleksandrina Goeva, Carly A. Martin + 6 more
The spatial organization of cells in tissue has a profound influence on their function, yet a high-throughput, genome-wide readout of gene expression with cellular resolution is lacking. Here, we introduce Slide-seq, a highly scalable method that enables facile generation of large volumes of unbiased spatial…
Kristen M. Naegle
The “presentation slide” is the building block of all academic presentations, whether they are journal clubs, thesis committee meetings, short conference talks, or hour-long seminars. A slide is a single page projected on a screen, usually built on the premise of a title, body, and figures or tables and includes both…
Tushar Aggarwal, Aarohi Bhand
In today's fast-paced world, effective presentations have become an essential tool for communication in both online and offline meetings. The crafting of a compelling presentation requires significant time and effort, from gathering key insights to designing slides that convey information clearly and concisely.…
Vincenzo Della Mea, Giulia L. Baroni, David Pilutti, Carla Di Loreto + 1 more
'Helmut Ahammer'] The digital slide, or Whole Slide Image, is a digital image, acquired with specific scanners, that represents a complete tissue sample or cytological specimen at microscopic level. While Whole Slide image analysis is recognized among the most interesting opportunities, the typical size of such…
Hazimeh, Adam, Wang, Ke + 8 more
Multimedia documents such as slide presentations and posters are designed to be interactive and easy to modify. Yet, they are often distributed in a static raster format, which limits editing and customization. Restoring their editability requires converting these raster images back into structured vector formats.…
Jiaxin Ge, Zora Zhiruo Wang, Xuhui Zhou, Yi-Hao Peng + 7 more
'Sanjay Subramanian' 'Qinyue Tan' 'Maarten Sap' 'Alane Suhr' 'Daniel Fried' 'Graham Neubig' 'Trevor Darrell'] Designing structured visuals such as presentation slides is essential for communicative needs, necessitating both content creation and visual planning skills. In this work, we tackle the challenge of automated…
Authors not listed
A thorough understanding of drug pharmacokinetics and target interaction within complex biological environments is critical for successful drug discovery. Quantitative matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI; qMSI) presents a promising avenue for such investigations. While…
Kimberly Ashman, Max S. Cooper, Huimin Zhuge, Sharon E. Fox + 4 more
Digital pathology, or the practice of acquiring, managing, and interpreting high-resolution digital images from glass pathology slides, holds much promise in precision medicine, potentially transforming diagnosis and prognosis based on computational image biomarkers derived from digital tissue images. However, for all…
Kang, Hyeonsu, Bao, Emily + 2 more
Vision-language models (VLMs) are increasingly used to evaluate multimodal content, including presentation slides, yet their slide-specific understanding remains underexplored despite their growing role as critics in agentic, model-forward pipelines. We introduce VLM-SlideEval, an evaluation framework that probes VLMs…
Yinhai Wang, Kate E. Williamson, Paul J. Kelly, Jacqueline A. James + 2 more
'Peter W. Hamilton' 'Indra Neil Sarkar'] Background Digital pathology provides a digital environment for the management and interpretation of pathological images and associated data. It is becoming increasing popular to use modern computer based tools and applications in pathological education, tissue based research…
Nobuhito Mori, Yoshihiro Miyazaki, Tatsuya Oda, Yasuyuki S. Kida + 1 more
'Fabio Baselice'] The creation of virtual slides, i.e., high-resolution digital images of biological samples, is expensive, and existing manual methods often suffer from stitching errors and additional reimaging costs. To address these issues, we propose a real-time mosaicing manager for manual microscopy (RT-4M) that…
Chris Gorman, Davide Punzo, Igor Octaviano, Steven Pieper + 5 more
'William J. R. Longabaugh' 'David A. Clunie' 'Ron Kikinis' 'Andrey Y. Fedorov' 'Markus D. Herrmann'] The exchange of large and complex slide microscopy imaging data in biomedical research and pathology practice is impeded by a lack of data standardization and interoperability, which is detrimental to the…
Kun Zhou, Jiakai He, Wenmian Yang, Zhensheng Wang + 2 more
Presentation slides are a primary medium for data-driven reporting, yet keeping complex, analytics-style decks up to date remains labor-intensive. Existing automation methods mostly follow fixed template filling and cannot support dynamic updates for diverse, user-authored slide decks. We therefore define "Dynamic…
Slawomir Walkowski, Janusz Szymas
Background There are many scanners of glass slides on the market now. Quality of digital images produced by them may be different and pathologists who examine virtual slides on a monitor may subjectively evaluate it. However, objective comparison of quality of digital slides captured by various devices requires…
Haodong Chen, Xuanhe Zhou, Wei Zhou, Xinyue Shao + 5 more
Automatically generating slide decks from source documents is an important application of large language models (LLMs). Existing benchmarks primarily assess slide completeness and technical depth, while overlooking the target audience as a critical real-world factor. For instance, specialists demand rigorous proofs…
James M. Dolezal, Sara Kochanny, Emma Dyer, Andrew Srisuwananukorn + 5 more
'Matteo Antonio Sacco' 'Frederick M. Howard' 'Anran Li' 'Prajval Mohan' 'Alexander T. Pearson'] Deep learning methods have emerged as powerful tools for analyzing histopathological images, but current methods are often specialized for specific domains and software environments, and few open-source options exist for…
Md Motaleb Hossen Manik, Md Zabirul Islam, Ge Wang
Modern vision–language models (VLMs) are increasingly used to interpret and generate educational content, yet their semantic outputs remain challenging to verify, reproduce, and audit over time. Inconsistencies across model families, inference settings, and computing environments undermine the reliability of…
Authors not listed
The analysis of molecular dynamics (MD) simulations is a critical but fragmented process, often requiring researchers to chain together multiple software tools and write bespoke scripts for routine structural and dynamic analyses. This workflow complexity creates a significant barrier to efficiency, standardization…
Cara J. Hawkins, Jon A. Newnham, Batoul Almoussawi, Nataliya L. Gulay + 8 more
Cara J. Hawkins 1 , Jon A. Newnham 1 , Batoul Almoussawi 1 , Nataliya L. Gulay 1 , Samuel L. Goodwin 1 , Marco Zanella 1 , Troy D. Manning 2 , Luke M. Daniels 2 , Matthew S. Dyer 2 , Tim D. Veal 3 , John B. Claridge 1 , Matthew J. Rosseinsky 1