23 papers · ranked by Valyu relevance
Chuqi Su, Yiming Gao, Yisu Zhou, Yiqin Sun + 3 more
'Bo Xiong'] Motivation: Light field microscopy is a compact solution to high-speed 3D fluorescence imaging. Usually, we need to do 3D deconvolution to the captured raw data. Although there are deep neural network methods that can accelerate the reconstruction process, the model is not universally applicable for all…
Arion Dey, Jared A. Weis, Victoria G. Weis
Histological analysis is crucial for understanding gastrointestinal (GI) tract homeostasis and disease pathophysiology. Various histological stains are commonly used in research settings for assessing development, disease pathogenesis, and therapeutic impacts. Specifically in the ordered architecture of the GI…
Varun Mannam, Yide Zhang, Yinhao Zhu, Evan Nichols + 6 more
Fluorescence microscopy imaging speed is fundamentally limited by the measurement signal-to-noise ratio (SNR). To improve image SNR for a given image acquisition rate, computational denoising techniques can be used to suppress noise. However, analytical techniques to estimate a denoised image from a single frame are…
Ariel Waisman
Quantitative analysis of fluorescence microscopy images is essential for studying expression levels, subcellular localization and co-occurrence of proteins and other biomolecules. While several automated tools exist for specific applications, there remains a need for user-friendly, customizable tools that can analyze…
Stephen J. Cross, Jordan D. J. R. Fisher, Mark A. Jepson
ModularImageAnalysis (MIA) is an ImageJ plugin providing a code-free graphical environment in which complex automated analysis workflows can be constructed and distributed. The near 200 included modules cover all stages of a typical analysis workflow, from image loading through image processing, object detection…
Jacob Trend, Fernando Alvarez Borges, Tali L. Babila
The application of micro-computed tomography (µCT) to foraminiferal test analysis has opened new avenues for high-resolution, non-destructive 3D characterisation of internal and external morphological features. However, existing workflows are typically limited by low throughput, manual segmentation, and reliance on…
Yoshitaka Kimori, Stacey D. Finley
RMPJ is an image-processing tool that facilitates the effective enhancement of low-contrast analysis objects and enables preprocessing to quantify the morphological features of the objects under analysis. This ImageJ plugin implements seven image-processing algorithms based on rotational morphological processing (RMP)…
Masoud Rahimi, Esmaeil Asadi Khameneh, Hamid Riazi-Esfahani, Tahereh Mahmoudi + 2 more
'Tahereh Mahmoudi' 'Elias Khalili Pour' 'Rahele Kafieh'] Background This study aimed to review the literature on the application of ImageJ in optical coherence tomography angiography (OCT-A) images. Methods A general search was performed in PubMed, Google Scholar, and Scopus databases. The authors evaluated each of the…
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…
Pierre Pouchin, Rayan Zoghlami, Rémi Valarcher, Maxence Delannoy + 5 more
'Manon Carvalho' 'Clémence Belle' 'Marc Mongy' 'Sophie Desset' 'Frédéric Brau'] The Open Microscopy Environment Remote Objects (OMERO) is an open-source image manager used by many biologists to store, organize, view, and share microscopy images, while the open-source software ImageJ/Fiji is a very popular program used…
Carlos García-López-de-Haro, Caterina Fuster-Barceló, Curtis Rueden, Jónathan Heras + 8 more
Mask annotation remains a significant bottleneck in AI-driven biomedical image analysis due to its labor-intensive nature. To address this challenge, we introduce SAMJ, a user-friendly ImageJ/Fiji plugin leveraging the Segment Anything Model (SAM). SAMJ enables seamless, interactive annotations with one-click…
Sankeert Satheesan, Jochen Gehrig, Laurent S.V. Thomas, Pablo Nicolás De Francesco
'Pablo Nicolás De Francesco'] Standardizing image datasets is essential for facilitating overall visual comparisons and enhancing compatibility with image-processing workflows. One way to achieve homogeneity for images containing a single object is to align the object to a common orientation. Here, we propose the…
Rocco D’Antuono, Giuseppina Pisignano
Bioimage analysis workflows allow the measurement of sample properties such as fluorescence intensity and polarization, cell number, and vesicles distribution, but often require the integration of multiple software tools. Furthermore, it is increasingly appreciated that to overcome the limitations of the 2D-view-based…
Michael Schmid, Florian Kraushofer, Alexander M. Imre, Tilman Kißlinger + 3 more
curves Authors: ['Michael Schmid' 'Florian Kraushofer' 'Alexander M. Imre' 'Tilman Kißlinger' 'Lutz Hammer' 'Ulrike Diebold' 'Michele Riva'] As part of the ViPErLEED project (Vienna package for Erlangen LEED, low-energy electron diffraction), computer programs have been developed for facile and user-friendly data…
Robert Haase, Elnaz Fazeli, David Legland, Michael Doube + 6 more
'S J Culley' 'Ilya Belevich' 'Eija Jokitalo' 'Martin Schorb' 'Anna H. Klemm' 'Christian Tischer'] Abstract: Modern research in the life sciences is unthinkable without computational methods for extracting, quantifying and visualizing information derived from biological microscopy imaging data. In the past decade, we…
Caterina Fuster-Barceló, Carlos García López de Haro, Estibaliz Gómez-de-Mariscal, Wei Ouyang + 3 more
This manuscript showcases the latest advancements in deepImageJ, a pivotal Fiji/ImageJ plugin for bioimage analysis in the life sciences. The plugin, known for its user-friendly interface, facilitates the application of diverse pre-trained neural networks to custom data. The manuscript demonstrates a number of…
Anna Kilian, Paweł Bilski, Małgorzata Sankowska
Background Remover (BGR) is a novel software tool developed as a plugin to the well-known ImageJ program and designed to address the challenges of analysing fluorescent microscopy images characterized by low signal-to-noise ratios and heterogeneous backgrounds. The used algorithm effectively differentiates between…
Gabriel J. Selzer, Curtis T. Rueden, Mark C. Hiner, Edward L. Evans + 12 more
Decades of iteration on scientific imaging hardware and software has yielded an explosion in not only the size, complexity, and heterogeneity of image datasets but also in the tooling used to analyze this data. This wealth of image analysis tools, spanning different programming languages, frameworks, and data…
Ling-Hong Hung, Evan Straw, Shishir Reddy, Zachary Colburn + 1 more
Biomedical image analyses can require many steps processing different types of data. Analysis of increasingly large data sets often exceeds the capacity of local computational resources. We present an easy-to-use and modular cloud platform that allows biomedical researchers to reproducibly execute and share complex…
Josh Moore, Daniela Basurto-Lozada, Sébastien Besson, John Bogovic + 65 more
A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process…
Ruman Gerst, Austin Mottola, Dhruv Khatri, Judith Berman + 1 more
Antimicrobial resistance and tolerance pose escalating global health threats, necessitating reproducible and accessible tools for antimicrobial susceptibility testing (AST). While disk diffusion assays (DDAs) and Epsilometer tests (Etests) are widely used, there are limited open-source tools to analyze them. We present…
Dawid Zamojski, Agnieszka Gogler‐Pigłowska, Dorota Ścieglińska, Michal Marczyk
differentiation markers on H-DAB-stained images of reconstructed human epidermis Authors: ['Dawid Zamojski' 'Agnieszka Gogler‐Pigłowska' 'Dorota Ścieglińska' 'Michal Marczyk'] Background: The integrity of the reconstructed human epidermis generated in vitro could be assessed using histological analyses combined with…
Authors not listed
nDTomo is a Python-based software suite for the simulation, reconstruction and analysis of X-ray chemical imaging and computed tomography data. It provides a collection of Python function-based tools designed for accessibility and education as well as a graphical user interface (GUI). Prioritising transparency and ease…