ArticleProtein science : a publication of the Protein Society2021
The ImageJ ecosystem: Open-source software for image visualization, processing, and analysis.
Article in Protein science : a publication of the Protein Society, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 172 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
172 citing papers in PubMed, 1 synthesis or guideline pooled it, 345 citations in OpenAlex.
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- Structural insights into a substrate translocation pathway revealed by the RND efflux pump complex MexJK fromScience advances · 2026Article
- Bidirectional control of vesicular GABA release, LTP, and amotivation by GluN2D-selective allosteric modulators and ketamine.Cell reports · 2026Article
- Connexin 43-dependent mesenchymal stem cell mitochondrial transfer activates PGC1α disrupting oxidative-inflammation axis in ischemia-reperfusion injury.Signal transduction and targeted therapy · 2026Article
- From Hummingbird to Elephant: Amyloid Formation in Natural Transthyretin Variants.bioRxiv : the preprint server for biology · 2026Article
- Genome-wide analysis of KCS gene family in sunflower reveals the involvement of HaKCS1-1 in wax biosynthesis and drought resistance.BMC plant biology · 2026Article
- Intramuscular Ketamine Pharmacokinetics in Humans: A Review.European journal of drug metabolism and pharmacokinetics · 2026Review
- A conserved in-frame stop codon acts as a multipotent defense mechanism in alphaviruses.Science advances · 2026Article
- Hafnium-Substituted Wells-Dawson Polyoxometalate as a High-Performance Contrast Agent for Transmission Electron Microscopy of Biological Ultrastructure.International journal of molecular sciences · 2026Article
- An Optimized and Systematically Integrated Expression, Extraction, and Purification Strategy Enabling Efficient Production of TCR-Like Antibodies in Escherichia coli.Current microbiology · 2026Article
- Emergence of Novel Reassortant H3N2 Avian Influenza Viruses in Southern China: Genetic Complexity and Pathogenicity in Chickens and Mice.Animals : an open access journal from MDPI · 2026Article
- Designing strategies for high-level production of peptide-N-glycosidase F (PNGase F) from Flavobacterium meningosepticum using high cell density fed-batch culture of E. coli.Bioprocess and biosystems engineering · 2026Article
- Review
- RNAi-Mediated Attenuation of CsCalS7-Related Transcripts Mitigates Callose Accumulation and Huanglongbing Symptoms.Molecular plant pathology · 2026Article
- Taurine reduces intracellular glucose accumulation in fructose-treated Caenorhabditis elegans.Amino acids · 2026Article
112 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 4 countries.
Funding
Abstract
For decades, biologists have relied on software to visualize and interpret imaging data. As techniques for acquiring images increase in complexity, resulting in larger multidimensional datasets, imaging software must adapt. ImageJ is an open-source image analysis software platform that has aided researchers with a variety of image analysis applications, driven mainly by engaged and collaborative user and developer communities. The close collaboration between programmers and users has resulted in adaptations to accommodate new challenges in image analysis that address the needs of ImageJ's diverse user base. ImageJ consists of many components, some relevant primarily for developers and a vast collection of user-centric plugins. It is available in many forms, including the widely used Fiji distribution. We refer to this entire ImageJ codebase and community as the ImageJ ecosystem. Here we review the core features of this ecosystem and highlight how ImageJ has responded to imaging technology advancements with new plugins and tools in recent years. These plugins and tools have been developed to address user needs in several areas such as visualization, segmentation, and tracking of biological entities in large, complex datasets. Moreover, new capabilities for deep learning are being added to ImageJ, reflecting a shift in the bioimage analysis community towards exploiting artificial intelligence. These new tools have been facilitated by profound architectural changes to the ImageJ core brought about by the ImageJ2 project. Therefore, we also discuss the contributions of ImageJ2 to enhancing multidimensional image processing and interoperability in the ImageJ ecosystem.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.