... an indispensable support community of enthusiasts on the ImageJ mailing list.Wayne Rasband is the core author of ImageJ; after developing the Macintosh-based National Institutes of ... made the brave decision of starting afresh with ImageJ using the Java programming language. By shifting to ... software from an individual operating system. To run ImageJ, a given system needs only the operating system- ... Sun or bundled with platform-specific installations of ImageJ (rsb.info.nih.gov/ij). With JRE available for most operating systems, ImageJ is platform-independent, running on Macintosh, Windows, Linux, ...
Tópico(s): Radiomics and Machine Learning in Medical Imaging
2007 - Future Science Ltd | BioTechniques
... cost effective answer for quantitative immunohistochemical analysis is ImageJ, developed by WayneRasband (http://imagej.nih.gov/ij/docs/index.html). ImageJ is a Java image processing and analysis program based on NIH Image for the Macintosh. ImageJ is available in the public domain (i.e., free). ImageJ runs on any computer that is a Java ... Microsystems or bundled with platform-specific installations of ImageJ (rsb.info.nih.gov/ij). Downloadable copies are ... OSX. For the evaluation of immunohistochemistry slides using ImageJ, images are captured onto the hard drive of ...
Tópico(s): MRI in cancer diagnosis
2013 - Wiley | The Anatomical Record
Petra Mlčochová, Sarah J. Caswell, Ian A. Taylor, Greg J. Towers, Ravindra K. Gupta,
... the automated cell-imaging system Hermes WiScan and ImageJ. On average, 104 cells were acquired and analysed ( ... an automated cell-imaging system Hermes WiScan and ImageJ (n = 3, mean ± s.e.m.). C. MDM ... using automated cell-imaging system Hermes WiScan and ImageJ. Addition of 20% ethanol for 10 min into ... an automated cell-imaging system Hermes WiScan and ImageJ and normalized to untreated control ˜100% (n = 3, ... an automated cell-imaging system Hermes WiScan and ImageJ (n = 4, mean ± s.e.m.; ***P-value ≤ ... the automated cell-imaging system Hermes WiScan and ImageJ 48 h post-infection (n = 3, mean ± s. ...
Tópico(s): Cytomegalovirus and herpesvirus research
2017 - Springer Nature | The EMBO Journal
Thomas Schmidt, Farzan Solimani, Robert Pollmann, Ronja Stein, Ansgar Schmidt, Inna Stulberg, Katja Kühn, Rüdiger Eming, Verena Eubel, P Kind, Nicole B. Arweiler, Cassian Sitaru, Michael Hertl,
... software (Soft Imaging System, Berlin, Germany) and free ImageJ software (imagej.nih.gov/ij/; see Fig E3). At ×100 ... GATA-3+ T cells). After generating a grid (ImageJ software; area per point, 50,000 square pixels), ... GATA-3+ T cells) adjacent to the BMZ (ImageJ software, cell counter; Fig E3, A), and their ... taken at ×200 magnification and after grid formation (ImageJ software; area per point, 50,000 square pixels) ... 4 squares in the BMZ and dermal region (ImageJ software, cell counter; Fig E3, B). BP180-NH2 ( ... in combination with CellˆD (Soft Imaging System) and ImageJ software. For counting of specifically stained T cells, ...
Tópico(s): Nail Diseases and Treatments
2018 - Elsevier BV | Journal of Allergy and Clinical Immunology
Isabella G. S. Visschers, Nicole M. van Dam, Janny L. Peters,
... leaf area, using freely available software such as ImageJ Fiji (https://fiji.sc) (Schindelin et al., 2012; ... leaf are too subtle to precisely quantify with ImageJ or Winfolia alone. As a result, thrips damage ... caused by thrips using two types of freeware, ImageJ (Schindelin et al., 2012) and Ilastik (Sommer et ... provided by the user (Sommer et al., 2011). ImageJ is often used to quantify the amount of ... and quantitation of feeding damage was performed with ImageJ Fiji (v.2.0.0 with Java 1. ... cut' in scans of individual leaf discs using ImageJ Fiji (Figure 1A). Before further processing in Ilastik, ...
Tópico(s): Plant Parasitism and Resistance
2018 - Wiley | Entomologia Experimentalis et Applicata
Tarik Exner, Carlo A. Beretta, Qi Gao, Cassian Afting, Inés Romero‐Brey, Ralf Bartenschlager, Leonard Fehring, Margarete Poppelreuther, Joachim Füllekrug,
... numbers or closely clustered. Here, we present an ImageJ-based approach for the detection and quantification of ... numbers or closely clustered. Here, we present an ImageJ-based approach for the detection and quantification of ... LDs were counted using the multipoint function of ImageJ/Fiji and saved as a region of interest ( ... using the BX41 widefield microscope setup and the ImageJ/Fiji plugin "Diffraction PSF 3D" (34Dougherty, R., 2005. ... integrated library and plugins for mathematical morphology with ImageJ.Bioinformatics. 2016; 32: 3532-3534Crossref PubMed Scopus (538) ...
Tópico(s): Plant biochemistry and biosynthesis
2019 - Elsevier BV | Journal of Lipid Research
Alexandra B. Schroeder, Ellen T. A. Dobson, Curtis Rueden, Pavel Tomančák, Florian Jug, Kevin W. Eliceiri,
... in larger multidimensional datasets, imaging software must adapt. ImageJ is an open‐source image analysis software platform ... in image analysis that address the needs of ImageJ's diverse user base. ImageJ consists of many components, some relevant primarily for ... 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 ... capabilities for deep learning are being added to ImageJ, reflecting a shift in the bioimage analysis community ...
Tópico(s): Single-cell and spatial transcriptomics
2020 - Wiley | Protein Science
Xu Wang, Jiahui Ni, Yan You, Guize Feng, Sulin Zhang, Weilian Bao, Hui Hou, Haidong Li, Lixin Liu, Mingyue Zheng, Yirui Wang, Hua Zhou, Weixing Shen, Xiaoyan Shen,
... was determined by immunoblots (A) and quantified by ImageJ software (B) (n = 3 independent experiments). The fold ... was determined by immunoblots (D) and quantified by ImageJ software (E) (n = 3 independent experiments). The fold ... intensity of E-cadherin staining was quantified by ImageJ software (H) (n = 3 independent experiments, n = 18 ... efficiency was confirmed by immunoblots and quantified by ImageJ software (n = 6 independent experiments). SNX10 was deleted ... efficiency was confirmed by immunoblots and quantified by ImageJ software (n = 6 independent experiments). Protein levels of ...
Tópico(s): Ion Transport and Channel Regulation
2021 - Springer Nature | The EMBO Journal
Dewei Jiang, Shu Wei, Fei Chen, Ying Zhang, Jiali Li,
... in panel (A) were quantified by use of ImageJ software. Data are presented as mean ± SEM (n = ... C and D) were quantified by use of ImageJ software. The 5hmC contents were quantified and calculated ... in panel (D) were quantified by use of ImageJ software. The 5mC contents were quantified and calculated ... in panel (A) were quantified by use of ImageJ software. Error bars denote standard deviations. *P < 0. ... in panel (D) were quantified by use of ImageJ software. n = 3 repetitions of the experiment. Source ... A and B) were quantified by use of ImageJ software. Data are presented as mean ± SEM (n = ...
Tópico(s): Genomics and Chromatin Dynamics
2017 - Springer Nature | EMBO Reports
Simon Dello, Ronald M. van Dam, Jules J.G. Slangen, Marcel C.G. van de Poll, Marc H.A. Bemelmans, Jan Willem W. M. Greve, Geerard L. Beets, Stephen J. Wigmore, Cornelis H.C. Dejong,
... expensive and usually requires support by a radiologist. ImageJ is a freely downloadable image analysis software package ... desktop. We aimed to assess the accuracy of ImageJ for hepatic CT volumetry. Methods ImageJ was downloaded from http://www.rsb.info.nih. ... metastases were retrospectively analyzed. Scans were opened in ImageJ; and the liver, all metastases, and the intended ... Volumes of virtual liver resection specimens measured with ImageJ were compared with specimen weights and calculated volumes ...
Tópico(s): MRI in cancer diagnosis
2007 - Springer Science+Business Media | World Journal of Surgery
Ryosuke Tajima, Yoichiro Kato,
... analysis requires costly special software (WinRHIZO). Novel freeware, ImageJ, has also been developed for the similar purpose, ... study compares the 16 algorithms available in the ImageJ for processing of rice root images. Among the ... binary method, where the coefficient of correlation between ImageJ-estimated and WinRHIZO-estimated root lengths is extremely ... r = 0.986). However, using the Triangle algorithm, ImageJ overestimated the rice root length compared with WinRHIZO. By multiplying the values obtained using ImageJ by 2/3, the estimates closely corresponded to ...
Tópico(s): Plant responses to water stress
2011 - Elsevier BV | Field Crops Research
Johannes Schindelin, Curtis Rueden, Mark Hiner, Kevin W. Eliceiri,
... and redistributed; in particular, the open-software platform ImageJ has had a huge impact on the life ... and continues to do so. From its inception, ImageJ has grown significantly due largely to being freely ... students, scientific staff, and advanced biology researchers use ImageJ on a daily basis, and exchange knowledge via its dedicated mailing list. Uses of ImageJ range from data visualization and teaching to advanced ... processing algorithms. In this review, we use the ImageJ project as a case study of how open- ...
Tópico(s): Image Processing Techniques and Applications
2015 - Wiley | Molecular Reproduction and Development
Curtis Rueden, Johannes Schindelin, Mark Hiner, Barry E. DeZonia, Alison E. Walter, Ellen T. Arena, Kevin W. Eliceiri,
ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ... recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur programmers, and ... requirements of modern science. We rewrote the entire ImageJ codebase, engineering a redesigned plugin mechanism intended to ... wider range of scientific requirements. This next-generation ImageJ, called "ImageJ2" in places where the distinction matters, ... functionality can be seamlessly integrated with the classic ImageJ interface, allowing users and developers to migrate to ...
Tópico(s): AI in cancer detection
2017 - BioMed Central | BMC Bioinformatics
Eleftherios I. Paschalis, Chengxin Zhou, Fengyang Lei, Nathan L. Scott, Vassiliki Kapoulea, Marie-Claude Robert, Demetrios G. Vavvas, Reza Dana, James Chodosh, Claes H. Dohlman,
... with Texas red (TUNEL+ cells) and quantified using ImageJ software version 1.43 or above (NIH, Bethesda, MD; http://imagej.nih.gov/ij) to measure the number of ... were produced, and axon degeneration was analyzed using ImageJ software, according to previous protocols.16Madigan M.C. ... antibody staining. TNF-α expression was quantified using ImageJ software on whole eye tissue cross sections stained ... was marked using the freehand selection tool from ImageJ software and according to DAPI boundaries. The enclosed ...
Tópico(s): Traumatic Brain Injury and Neurovascular Disturbances
2017 - Elsevier BV | American Journal Of Pathology
Levi Teigen, Adam J. Kuchnia, Emily Nagel, Christopher Deuth, David M. Vock, Urvashi Mulasi, Carrie P. Earthman,
... used. We also demonstrate the importance of the ImageJ corrigendum published in this journal. Methods Two software programs, National Institutes of Health ImageJ and Tomovision sliceOmatic, were compared. ImageJ measures were obtained using both the original tutorial ... 0.985–1.000). The overall mean difference (ImageJ tutorial with corrigendum − sliceOmatic) for the entire sample ( ... 2.47 cm 2 ). The overall mean difference (ImageJ corrected − original) for the entire sample (N = 51) ... to be ∼1.53 cm 2 higher with ImageJ than sliceOmatic. This difference was not found to ...
Tópico(s): Frailty in Older Adults
2017 - Wiley | Journal of Parenteral and Enteral Nutrition
Wonkyung Cho, Sharad K. Mittal, Elsayed Elbasiony, Sunil K. Chauhan,
... number of mast cells (avidin+) was calculated using ImageJ version 1.52v software (NIH, Bethesda, MD; https://imagej.nih.gov/ij, last accessed November 20, 2020). ... was calculated using the vessel analysis plugin in ImageJ version 1.52v. Unpaired two-tailed t-tests ... were generated to quantify vascular density using the ImageJ version 1.52v software. Nasal suture resulted in ... covered by the new branching blood vessels using ImageJ version 1.52v software. Consistent with previous clinical ... numbers of avidin+ mast cells were quantified using ImageJ version 1.52v software. A significantly higher number ...
Tópico(s): melanin and skin pigmentation
2021 - Elsevier BV | American Journal Of Pathology
Raziyeh Mahmoudzadeh, Mirataollah Salabati, Khan Ma, Sunir J. Garg, Jason Hsu,
... macular degeneration (AMD) using Heidelberg Eye Explorer and ImageJ software.Fundus autofluorescence (FAF) images of eyes with ... and semi-automated (RegionFinder) software, as well as ImageJ manual and semi-automated (Color Threshold) software.Fifty- ... mm2 and 9.75 (10.3) mm2 using ImageJ manual and semi-automated tools, respectively. Compared with ... and 0.16 mm2 with manual Heidelberg, manual ImageJ, and semi-automated ImageJ measurements, respectively. Homogeneous GA lesions showed less disparity ... measurements across modalities compared with non-homogeneous lesions.ImageJ appears to be a reliable tool for GA ...
Tópico(s): Glaucoma and retinal disorders
2021 - Association for Research in Vision and Ophthalmology | Translational Vision Science & Technology
Raziyeh Mahmoudzadeh, Mirataollah Salabati, Jason Hsu, Khan Ma,
... CFT) measurements using the Heidelberg Eye Explorer and ImageJ software. Methods Optical coherence tomography (OCT) images were ... measured the CFT of the same images using ImageJ software. A Pearson correlation coefficient, intraclass correlation coefficient, ... and correlation between the Heidelberg Eye Explorer and ImageJ measurements. Results One-hundred and twenty-two OCT ... caliper tool was 264.8 ± 113 µm. Using ImageJ software, graders 1 and 2 obtained mean CFT ... than 4 µm mean difference between Heidelberg and ImageJ CFT values (2.67 ± 3.46 and 3. ...
Tópico(s): Retinal Diseases and Treatments
2021 - Elsevier BV | Canadian Journal of Ophthalmology
James R. Roush, Karen C. Bustillo, Ellen Low,
... measuring Q-angles using a goniometer and the IMAGEJ program, a public domain program developed at the ... data using the National Institute of Health (NIH) IMAGEJ computer program. Quadriceps angles measured bilaterally for 30 ... 2,1) for measuring Q-angle with the IMAGEJ program was .98 (SEM = 1.05°). The ICC ( ... between measures obtained with a goniometer versus the IMAGEJ program was .89 (SEM = 2.06°). Conclusions: There ... to those obtained with computer-assistance using the IMAGEJ program. There may be a bias on the ...
Tópico(s): Foot and Ankle Surgery
2008 - Nova Southeastern University | Internet Journal of Allied Health Sciences and Practice
Simon Dello, Jan H.M.B. Stoot, Rogier S. A. van Stiphout, Johanne G. Bloemen, Stephen J. Wigmore, Cornelis H.C. Dejong, Ronald M. van Dam,
... an important risk factor for posthepatectomy liver failure. ImageJ and OsiriX® are both free, open-source image ... aim of the present study was to compare ImageJ and OsiriX® in performing prospective computed tomography (CT) ... liver, tumor, and future resection specimen prospectively with ImageJ and OsiriX®. A radiologist also measured these volumes ... resection specimens and the volumes calculated prospectively with ImageJ and OsiriX® (r=0.89; r=0.83, ... radiological software iNtuition® and the volumes measured with ImageJ and OsiriX® (r=0.93; r=0.95, ...
Tópico(s): Advanced X-ray and CT Imaging
2010 - Springer Science+Business Media | World Journal of Surgery
Brian A. Irving, Judy Y. Weltman, David W. Brock, Christopher K. Davis, Glenn A. Gaesser, Arthur Weltman,
... areas obtained using Slice‐O‐Matic and NIH ImageJ medical imaging software packages. Research Methods and Procedures: ... 2.6% for Slice‐O‐Matic and NIH ImageJ, respectively, with intra‐ and inter‐investigator coefficients of ... cm 2 using Slice‐O‐Matic and NIH ImageJ. Bland‐Altman analyses revealed that Slice‐O‐Matic and NIH ImageJ results were comparable. The mean differences (95% confidence ... obtained using the Slice‐O‐Matic and NIH ImageJ medical imaging software were +2.5 cm 2 (− ... that both the Slice‐O‐Matic and NIH ImageJ medical imaging software systems provide reliable measurements of ...
Tópico(s): Cardiovascular Disease and Adiposity
2007 - Wiley | Obesity
Ning Yang, Rachel Mosher, Songwon Seo, David J. Beebe, Andreas Friedl,
... fiber was measured using an angle measurement tool (ImageJ; http://rsbweb.nih.gov/ij/). Two observers measured ... The number of attached cells was determined using ImageJ software (ImageJ), and the average value obtained on the FN ... using an inverted microscope (Olympus) and analyzed using ImageJ software. Live MDA-MB-231 cells were labeled ... BD Biosciences). The resulting images were stacked using ImageJ software (ImageJ). The migratory directionality of each individual cell was ... cell center using the Fragment Line tool in ImageJ. The results represent the average of two to ...
Tópico(s): Skin and Cellular Biology Research
2011 - Elsevier BV | American Journal Of Pathology
Produção Nacional
Revisado por pares
Mírian Cristina Gomes Costa, Isabela Maria de Lima Cunha, Lúcio André de Castro Jorge, Isabel Cristina da Silva Araújo,
... systems have been developed to analyze digital images. ImageJ and Safira are public-domain systems that may ... roots. However, differences in root properties measured using ImageJ and Safira are supposed. This study compared values ... replications. Root images were digitized and the systems ImageJ and Safira used to determine root length and ... the confidence interval and t-test. Both systems ImageJ and Safira had positive correlation coefficients with the ... to 0.80, with lowest value observed for ImageJ in the measurement of surface area of roots ...
Tópico(s): Soil Management and Crop Yield
2014 - Sociedade Brasileira de Ciência do Solo | Revista Brasileira de Ciência do Solo
Shutang Zhou, Esther Nissao, Isabel L. Jackson, Wei Leong, Lindsay Dancy, Frank Cuttitta, Željko Vujašković, Mary E. Sunday,
... of immunohistochemistry (IHC) by using image analysis with ImageJ version 1.46e (NIH, Bethesda, MD) to determine ... field being 2 and <20 μm by using ImageJ version 1.46e. The total area of tissue ... that are not recognized as separate cells by ImageJ. This was achieved by counting numbers of nuclei ... and 20 weeks later. Bright field microscopy and ImageJ screening demonstrated altered numbers of immunopositive cells as ... vascular smooth muscle. In subpleural lung (photomicrographs for ImageJ), a few small blood vessels are present. B: ...
Tópico(s): Cancer, Stress, Anesthesia, and Immune Response
2013 - Elsevier BV | American Journal Of Pathology
Attila E. Farkas, Roland S. Hilgarth, Christopher Capaldo, Christian Gerner‐Smidt, Doris R. Powell, Paula M. Vertino, Michael Koval, Charles A. Parkos, Asma Nusrat,
... The films were scanned and subsequently processed using ImageJ version 1.46d (NIH, Bethesda, MD; http://imagej.nih.gov/ij),12Abramoff M.D. Magalhaes P.J. Ram S.J. Image processing with ImageJ.Biophotonics Int. 2004; 11: 36-42Google Scholar with ... plugin (available at image.bio.methods.free.fr/ImageJ/?Protein-Array-Analyzer-for-ImageJ.html, last accessed April 8, 2015).13Carpentier G, Henault E: Protein array analyzer for ImageJ. Proceedings of the ImageJ User and Developer Conference, Centre de Recherche Public ...
Tópico(s): Gut microbiota and health
2015 - Elsevier BV | American Journal Of Pathology
P. A. Sokolov, M. V. Belousov, Stanislav A. Bondarev, Galina A. Zhouravleva, Nina A. Kasyanenko,
... developed an open-source FibrilJ plugin for the ImageJ/FiJi program. It automatically recognizes the fibrils on ... 1 Licensing provisions: Apache-2.0 Programming language: ImageJ Macro Language Nature of problem: Amyloids are large ... due to the human factor, are insufficiently representative. ImageJ/FiJi is open-source software and one of ... most commonly used program for image processing. The ImageJ/FiJi community provides BoneJ plugin for bones analysis ... were used to determine their persistence lengths using ImageJ/FiJi. These above mentioned plugins are not designed ...
Tópico(s): Bioinformatics and Genomic Networks
2017 - Elsevier BV | Computer Physics Communications
Deepa Mane, AlkaD Kale, Chetan Belaldavar,
... trials. Hence, we aimed to quantify IHC by ImageJ analysis with a novel IHC profiler plugin. ImageJ has not been tried in oral precancerous tissues ... tissues and oral squamous cell carcinoma (OSCC) using ImageJ software with IHC profiler plugin.Materials and Methods: ... IHC staining for TN-C and image acquisition, ImageJ analysis was performed as per the standard recommended ... can now be quantified using freely downloadable software ImageJ analysis in oral precancerous tissues and OSCC. This ... propose that IHC markers should be quantified using ImageJ by our entire oral pathology fraternity so as ...
Tópico(s): Oral and Maxillofacial Pathology
2017 - Medknow | Journal of Oral and Maxillofacial Pathology
Lauren Richardson, Gracie Vargas, Tyra Brown, Lorenzo Ochoa, Samantha Sheller‐Miller, George R. Saade, Robert N. Taylor, Ramkumar Menon,
... second harmonic generation microscopy. Images were analyzed using ImageJ and IMARIS software. Three-dimensional microscopic analysis of ... second harmonic generation microscopy. Images were analyzed using ImageJ and IMARIS software. Three-dimensional microscopic analysis of ... epithelial shedding and gaps, and collagen alterations using ImageJ software bundled with 64-bit Java version 1.8.0_112 (NIH, Bethesda, MD; http://imagej.nih.gov/ij), whereas IMARIS software version 7. ... 20) Google Scholar) and stitching them together with ImageJ. The center nine images, captured with a 25× ...
Tópico(s): Pregnancy and preeclampsia studies
2017 - Elsevier BV | American Journal Of Pathology
Dominica Dian Saraswati Sumantri, Ria Noerianingsih Firman, A. Azhari,
Periapical abscess radiography analysis using imageJ after endodontics treatment. The visual assessment to measure the lesion of periapical abscesses on the radiograph interpretation has the distinction of ... on periapical abscess through digitization periapical radiograph using ImageJ software. This research have a form of observational ... Padjadjaran University Bandung. The radiograph will digitized using ImageJ software to get the extensive of lesions, the ... abses periapikal melalui digitalisasi radiograf periapikal menggunakan software ImageJ . Penelitian bersifat analisis observasional. Sampel diambil sebanyak masing- ...
Tópico(s): Endodontics and Root Canal Treatments
2017 - Gadjah Mada University | Majalah Kedokteran Gigi Indonesia
César Domínguez, Jónathan Heras, Vico Pascual,
... a bridge to connect two of those tools: ImageJ, a program for image analysis in life sciences, ... library. Methods. Based on a thorough analysis of ImageJ and OpenCV, we detected the features of these ... employed to create applications combining features from both ImageJ and OpenCV. From the perspective of ImageJ developers, they can use IJ-OpenCV to easily ... developers, this library provides a link to the ImageJ graphical user interface and all its features to ... The IJ-OpenCV library bridges the gap between ImageJ and OpenCV, allowing the connection and the cooperation ...
Tópico(s): Digital Imaging for Blood Diseases
2017 - Elsevier BV | Computers in Biology and Medicine