A5032461862- Cell Image Analysis Techniques
- Genetics, Bioinformatics, and Biomedical Research
- Scientific Computing and Data Management
- Radiomics and Machine Learning in Medical Imaging
- Image Processing Techniques and Applications
- Advanced Fluorescence Microscopy Techniques
- AI in cancer detection
- Medical Image Segmentation Techniques
- Single-cell and spatial transcriptomics
- Distributed and Parallel Computing Systems
- Advanced Surface Polishing Techniques
- Graphite, nuclear technology, radiation studies
- Advanced Image and Video Retrieval Techniques
- Biomedical Text Mining and Ontologies
- Renal Transplantation Outcomes and Treatments
- Neural Networks and Applications
- Theoretical and Computational Physics
- Metal Forming Simulation Techniques
- Research Data Management Practices
- Clinical Laboratory Practices and Quality Control
- Advanced Vision and Imaging
- Geological and Geophysical Studies
- Computer Graphics and Visualization Techniques
- Biomedical and Engineering Education
- Computational Physics and Python Applications
University of Minnesota
2025
University of Wisconsin–Madison
2013-2024
Optica
2016-2021
ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, extensible plug-in architecture, enjoys contributions from non-programmers, amateur programmers, professional developers alike. Enabling such a diversity contributors has resulted large community that spans physical sciences. However, rapidly growing user base, diverging plugin suites, technical limitations have revealed clear need for concerted...
In the field of fluorescence microscopy, there is continued demand for dynamic technologies that can exploit complete information from every pixel an image. One imaging technique with proven ability yielding additional Fluorescence Lifetime Imaging Microscopy (FLIM). FLIM allows measurement how long a fluorophore stays in excited energy state, and this affected by changes its chemical microenvironment, such as proximity to other fluorophores, pH, hydrophobic regions. This provide about...
CellProfiler is a widely used software for creating reproducible, reusable image analysis workflows without needing to code. In addition the >90 modules that make up main program, has plugins system allows creation of new which integrate with other Python tools or are packaged in containers. The CellProfiler-plugins repository contains number these modules, especially experimental and/or dependency-heavy. Here, we present an upgraded repository, example accessing containerised tools,...
Abstract Background No gold standard exists in the world of scientific image acquisition; a proliferation instruments each with its own proprietary data format has made out-of-the-box sharing that nearly impossible. In field light microscopy, Bio-Formats library was designed to translate such formats common, open-source schema, enabling and reproduction results. While proved successful for microscopy images, greater community lacking domain-independent framework translation. Results SCIFIO...
Abstract Summary ImageJ-MATLAB is a lightweight Java library facilitating bi-directional interoperability between MATLAB and ImageJ. By defining standard for translation matrix image data structures, researchers are empowered to select the best tool their image-analysis tasks. Availability Implementation Freely available extension ImageJ2 (http://imagej.net/Downloads). Installation use instructions at http://imagej.net/MATLAB_Scripting. Tested with ImageJ 2.0.0-rc-54, 1.8.0_66 R2015b....
Abstract ImageJ provides a framework for image processing across scientific domains while being fully open source. Over the years has been substantially extended to support novel applications in imaging as they emerge, particularly area of biological microscopy, with functionality made more accessible via Fiji distribution ImageJ. Within this software ecosystem, work done extend accessibility utilize scripting, macros, and plugins variety programming scenarios, e.g., from Groovy Python...
ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, extensible plug-in architecture, enjoys contributions from non-programmers, amateur programmers, professional developers alike. Enabling such a diversity contributors has resulted large community that spans physical sciences. However, rapidly growing user base, diverging plugin suites, technical limitations have revealed clear need for concerted...
Abstract In the field of fluorescence microscopy, there is continued demand for dynamic technologies that can exploit complete information from every pixel an image. One imaging technique with proven ability yielding additional Fluorescence Lifetime Imaging Microscopy (FLIM). FLIM allows measurement how long a fluorophore stays in excited energy state and affected by changes its chemical microenvironment, such as proximity to other fluorophores, pH, hydrophobic regions. This provide about...
Many scientific software platforms provide plugin mechanisms that simplify the integration, deployment, and execution of externally developed functionality. One most widely used in imaging space is Fiji, a popular open-source application for image analysis. Fiji incorporates builds on ImageJ ImageJ2 platforms, which powerful architecture by thousands plugins to solve wide variety problems. This capability major part Fiji's success, it has become biological analysis tool target new However,...
Decades of iteration on scientific imaging hardware and software has yielded an explosion in not only the size, complexity, heterogeneity image datasets but also tooling used to analyze this data. This wealth analysis tools, spanning different programming languages, frameworks, data structures, is itself a problem for analysts who must adapt new technologies integrate established routines solve increasingly complex problems. While many “bridge” layers exist unify pairs popular there exists...