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{\mu}Manager, an open-source microscopy acquisition software, has been an essential tool for many microscopy experiments over the past 15 years, but is not easy to use for experiments in which image acquisition and analysis are closely…

Quantitative Methods · Quantitative Biology 2024-02-12 Henry Pinkard , Nico Stuurman , Laura Waller

The computer programs most users interact with daily are driven by a graphical user interface (GUI). However, many scientific applications are used with a command line interface (CLI) for the ease of development and increased flexibility…

Human-Computer Interaction · Computer Science 2008-06-03 N. C. Manoukis , E. C. Anderson

MATI (Microstructural Analysis Toolbox for Imaging) is a versatile MATLAB-based toolbox that combines both simulation and data fitting capabilities for microstructural dMRI research. It provides a user-friendly, GUI-driven interface that…

In this paper, we describe a Graphical User Interface (GUI) designed to manage large quantities of image data of a biological system. After setting the design requirements for the system, we developed an ecology quantification GUI that…

Quantitative Methods · Quantitative Biology 2008-01-08 Nigel J. Burroughs , George D. Tsibidis , William Gaze , Liz Wellington

VISSIM is a widely used microscopic traffic simulator, which not only provides a graphical user interface to simulate simple static controls (pre-timed or fixed-time) but also offers flexibility to dynamically control simulation through…

Systems and Control · Electrical Eng. & Systems 2020-07-31 Prateek Bansal

This paper presents a Matlab toolbox to perform basic image processing and visualization tasks, particularly designed for medical image processing. The functionalities available are similar to basic functions found in other non-Matlab…

Mathematical Software · Computer Science 2021-04-13 Alberto Gomez

Providing high-quality electron images and hyperspectral X-ray maps is a focus of many modern electron microscopy laboratories. Nevertheless, further image processing and annotations are often needed to prepare them for publications and…

Image and Video Processing · Electrical Eng. & Systems 2021-03-24 Noah Kraft , Anette von der Handt

Graphical user interface (GUI) has become integral to modern society, making it crucial to be understood for human-centric systems. However, unlike natural images or documents, GUIs comprise artificially designed graphical elements arranged…

Computer Vision and Pattern Recognition · Computer Science 2025-03-19 Ziwei Wang , Weizhi Chen , Leyang Yang , Sheng Zhou , Shengchu Zhao , Hanbei Zhan , Jiongchao Jin , Liangcheng Li , Zirui Shao , Jiajun Bu

In this paper we introduce the responsive graphical user interface (ReGUI) approach to creating applications, and demonstrate how this approach can be implemented in MATLAB. The same general technique can be used in other programming…

Human-Computer Interaction · Computer Science 2026-04-10 Matej Mikulszky , Jana Pocsova , Andrea Mojzisova , Igor Podlubny

The open-source console MaRCoS, which stands for "Magnetic Resonance Control System", combines hardware, firmware and software elements for integral control of Magnetic Resonance Imaging (MRI) scanners. Previous developments have focused on…

Medical Physics · Physics 2025-07-29 J. M. Algarín , T. Guallart-Naval , J. Borreguero , F. Galve , J. Alonso

We present Spectral GUI, a multiplatform breast MR image analysis tool designed to facilitate the segmentation of fibro glandular tissues and lesions in T1 weighted breast MR images via a graphical user interface (GUI). Spectral GUIR uses…

Image and Video Processing · Electrical Eng. & Systems 2020-04-21 Prajval Koul

We present a user-friendly software for photonic analog quantum computing with an installable MATLAB package and the graphical user interface (GUI) that allows for convenient operation without requiring programming skills. Arbitrary…

Quantum Physics · Physics 2018-10-05 Hao Tang , Yan-Yan Zhu , Jun Gao , Marcus Lee , Peng-Cheng Lai , Xian-Min Jin

With the continuing advances in scientific instrumentation, scanning microscopes are now able to image physical systems with up to sub-atomic-level spatial resolutions and sub-picosecond time resolutions. Commensurately, they are generating…

Real time computer control is an essential feature of scanning probe microscopes, which have become essential tools for the characterization and investigation of nanometer scale samples. Most commercial (and some open-source) scanning probe…

Mesoscale and Nanoscale Physics · Physics 2013-01-24 Venkat Chandrasekhar , Manan Mehta

Photoacoustic (PA) imaging systems based on clinical linear ultrasound arrays have become increasingly popular in translational PA research. Such systems can be more easily integrated in a clinical workflow due to the simultaneous access to…

In today's world of big data, computational analysis has become a key driver of biomedical research. Recent exponential growth in the volume of available omics data has reshaped the landscape of contemporary biology, creating demand for a…

Distributed, Parallel, and Cluster Computing · Computer Science 2019-12-09 Jaqueline J. Brito , Thiago Mosqueiro , Jeremy Rotman , Victor Xue , Douglas J. Chapski , Juan De la Hoz , Paulo Matias , Lana Martin , Alex Zelikovsky , Matteo Pellegrinni , Serghei Mangul

Graphical User Interface (GUI) agents, powered by Large Foundation Models, have emerged as a transformative approach to automating human-computer interaction. These agents autonomously interact with digital systems or software applications…

Microscopes have morphed from purely optical instruments into motorized, robotic machines that form images on digital sensors rather than eyeballs. This continuing trend towards automation and digitization enables many new approaches to…

Other Quantitative Biology · Quantitative Biology 2020-05-04 Raghav Chhetri , Stephan Preibisch , Nico Stuurman

Utilizing Graphic User Interface (GUI) for human-computer interaction is essential for accessing a wide range of digital tools. Recent advancements in Vision Language Models (VLMs) highlight the compelling potential to develop versatile…

Artificial Intelligence · Computer Science 2025-06-02 Wentong Chen , Junbo Cui , Jinyi Hu , Yujia Qin , Junjie Fang , Yue Zhao , Chongyi Wang , Jun Liu , Guirong Chen , Yupeng Huo , Yuan Yao , Yankai Lin , Zhiyuan Liu , Maosong Sun

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 observed a dramatic increase…

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