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Brahmadhi, Ageng, and Ira Citra Ningrom. "Comparative Analysis of Kidney Histomorphometry Utilizing Two Distinct Image Processing Software." Journal of Biomedicine and Translational Research 9, no. 3 (2023): 104–10. http://dx.doi.org/10.14710/jbtr.v9i3.18554.
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ABSTRACTBackground: Histopathological examination is critical to evaluate tissue condition. An accurate assessment is necessary for diagnosis establishment. Nowadays, both quantitative and qualitative scoring are enhanced with computer-assisted image analysis to reduce bias. Various software was developed to assist in image analysis. The question of whether the measurement results from one software will be comparable to those from another software may come up, given the wide variety of software options. Nevertheless, this subject is only occasionally discussed.Objective: This study aimed to compare the measurement results from Fiji and QuPath software in kidney histomorphometry.Methods: Normal kidney histological slide was observed. Selected histological structures, including the renal corpuscle area, glomerular area, Bowman space area, inner diameter of proximal, distal, and Henle loop, were measured using QuPath and Fiji software. The measurement results from the two software were compared for value differences and agreement analysis.Results: The renal corpuscle means the area was 12.7x103 µm2 in QuPath and 12.5 x103 µm2 in Fiji. The glomerular area was 7.8 x103 µm2 for both software. The proximal tubule's inner diameters varied from 18.7 to 150.8 µm. Smaller inner diameters were observed in distal tubules (17.1-80.5 µm) and The Henle loop (15.5-69.6 µm). There was no significant difference in measurement results of particular structures between the compared software (P-value > 0.05). The further confirmational analysis supported the similarity between the two measurement results.Conclusion: the measurement result of kidney microstructures using QuPath and Fiji were identical.
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Thomas, Laurent S. V., Franz Schaefer, and Jochen Gehrig. "Fiji plugins for qualitative image annotations: routine analysis and application to image classification." F1000Research 9 (February 12, 2021): 1248. http://dx.doi.org/10.12688/f1000research.26872.2.
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Quantitative measurements and qualitative description of scientific images are both important to describe the complexity of digital image data. While various software solutions for quantitative measurements in images exist, there is a lack of simple tools for the qualitative description of images in common user-oriented image analysis software. To address this issue, we developed a set of Fiji plugins that facilitate the systematic manual annotation of images or image-regions. From a list of user-defined keywords, these plugins generate an easy-to-use graphical interface with buttons or checkboxes for the assignment of single or multiple pre-defined categories to full images or individual regions of interest. In addition to qualitative annotations, any quantitative measurement from the standard Fiji options can also be automatically reported. Besides the interactive user interface, keyboard shortcuts are available to speed-up the annotation process for larger datasets. The annotations are reported in a Fiji result table that can be exported as a pre-formatted csv file, for further analysis with common spreadsheet software or custom automated pipelines. To illustrate possible use case of the annotations, and facilitate the analysis of the generated annotations, we provide examples of such pipelines, including data-visualization solutions in Fiji and KNIME, as well as a complete workflow for training and application of a deep learning model for image classification in KNIME. Ultimately, the plugins enable standardized routine sample evaluation, classification, or ground-truth category annotation of any digital image data compatible with Fiji.
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Thomas, Laurent S. V., Franz Schaefer, and Jochen Gehrig. "Fiji plugins for qualitative image annotations: routine analysis and application to image classification." F1000Research 9 (October 15, 2020): 1248. http://dx.doi.org/10.12688/f1000research.26872.1.
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Quantitative measurements and qualitative description of scientific images are both important to describe the complexity of digital image data. While various software solutions for quantitative measurements in images exist, there is a lack of simple tools for the qualitative description of images in common user-oriented image analysis software. To address this issue, we developed a set of Fiji plugins that facilitate the systematic manual annotation of images or image-regions. From a list of user-defined keywords, these plugins generate an easy-to-use graphical interface with buttons or checkboxes for the assignment of single or multiple pre-defined categories to full images or individual regions of interest. In addition to qualitative annotations, any quantitative measurement from the standard Fiji options can also be automatically reported. Besides the interactive user interface, keyboard shortcuts are available to speed-up the annotation process for larger datasets. The annotations are reported in a Fiji result table that can be exported as a pre-formatted csv file, for further analysis with common spreadsheet software or custom automated pipelines. To facilitate and spread the usage of analysis tools, we provide examples of such pipelines, including a complete workflow for training and application of a deep learning model for image classification in KNIME. Ultimately, the plugins enable standardized routine sample evaluation, classification, or ground-truth category annotation of any digital image data compatible with Fiji.
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Davis, Janel L., Brian Soetikno, Ki-Hee Song, Yang Zhang, Cheng Sun, and Hao F. Zhang. "RainbowSTORM: an open-source ImageJ plug-in for spectroscopic single-molecule localization microscopy (sSMLM) data analysis and image reconstruction." Bioinformatics 36, no. 19 (2020): 4972–74. http://dx.doi.org/10.1093/bioinformatics/btaa635.
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Abstract Summary Spectroscopic single-molecule localization microscopy (sSMLM) simultaneously captures the spatial locations and full spectra of stochastically emitting fluorescent single molecules. It provides an optical platform to develop new multimolecular and functional imaging capabilities. While several open-source software suites provide subdiffraction localization of fluorescent molecules, software suites for spectroscopic analysis of sSMLM data remain unavailable. RainbowSTORM is an open-source ImageJ/FIJI plug-in for end-to-end spectroscopic analysis and visualization for sSMLM images. RainbowSTORM allows users to calibrate, preview and quantitatively analyze emission spectra acquired using different reported sSMLM system designs and fluorescent labels. Availability and implementation RainbowSTORM is a java plug-in for ImageJ (https://imagej.net)/FIJI (http://fiji.sc) freely available through: https://github.com/FOIL-NU/RainbowSTORM. RainbowSTORM has been tested with Windows and Mac operating systems and ImageJ/FIJI version 1.52. Supplementary information Supplementary data are available at Bioinformatics online.
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Nayak, U. P., M. Müller, D. Britz, M. A. Guitar, and F. Mücklich. "Image Processing using Open Source Tools and their Implementation in the Analysis of Complex Microstructures." Practical Metallography 58, no. 8 (2021): 484–506. http://dx.doi.org/10.1515/pm-2021-0039.
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Abstract Considering the dependance of materials’ properties on the microstructure, it is imperative to carry out a thorough microstructural characterization and analysis to bolster its development. This article is aimed to inform the users about the implementation of FIJI, an open source image processing software for image segmentation and quantitative microstructural analysis. The rapid advancement of computer technology in the past years has made it possible to swiftly segment and analyze hundreds of micrographs reducing hours’ worth of analysis time to a mere matter of minutes. This has led to the availability of several commercial image processing software programs primarily aimed at relatively inexperienced users. Despite the advantages like ‘one-click solutions’ offered by commercial software, the high licensing cost limits its widespread use in the metallographic community. Open-source platforms on the other hand, are free and easily available although rudimentary knowledge of the user-interface is a pre-requisite. In particular, the software FIJI has distinguished itself as a versatile tool, since it provides suitable extensions from image processing to segmentation to quantitative stereology and is continuously developed by a large user community. This article aims to introduce the FIJI program by familiarizing the user with its graphical user-interface and providing a sequential methodology to carry out image segmentation and quantitative microstructural analysis.
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Hartrampf, Philipp E., Marieke Heinrich, Anna Katharina Seitz, et al. "Metabolic Tumour Volume from PSMA PET/CT Scans of Prostate Cancer Patients during Chemotherapy—Do Different Software Solutions Deliver Comparable Results?" Journal of Clinical Medicine 9, no. 5 (2020): 1390. http://dx.doi.org/10.3390/jcm9051390.
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(1) Background: Prostate-specific membrane antigen (PSMA)-derived tumour volume (PSMA-TV) and total lesion PSMA (TL-PSMA) from PSMA PET/CT scans are promising biomarkers for assessing treatment response in prostate cancer (PCa). Currently, it is unclear whether different software tools for assessing PSMA-TV and TL-PSMA produce comparable results. (2) Methods: 68Ga-PSMA PET/CT scans from n = 21 patients with castration-resistant PCa (CRPC) receiving chemotherapy were identified from our single-centre database. PSMA-TV and TL-PSMA were calculated with Syngo.via (Siemens) as well as the freely available Beth Israel plugin for FIJI (Fiji Is Just ImageJ) before and after chemotherapy. While statistical comparability was illustrated and quantified via Bland-Altman diagrams, the clinical agreement was estimated by matching PSMA-TV, TL-PSMA and relative changes of both variables during chemotherapy with changes in serum PSA (ΔPSA) and PERCIST (Positron Emission Response Criteria in Solid Tumors). (3) Results: Comparing absolute PSMA-TV and TL-PSMA as well as Bland–Altman plotting revealed a good statistical comparability of both software algorithms. For clinical agreement, classifying therapy response did not differ between PSMA-TV and TL-PSMA for both software solutions and showed highly positive correlations with BR. (4) Conclusions: due to the high levels of statistical and clinical agreement in our CRPC patient cohort undergoing taxane chemotherapy, comparing PSMA-TV and TL-PSMA determined by Syngo.via and FIJI appears feasible.
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Naqvi, Tanveer Haider. "Status and Impact of Social Media and Networking Sites on Students of College of Medicine Nursing and Health Sciences." DESIDOC Journal of Library & Information Technology 39, no. 4 (2019): 187–91. http://dx.doi.org/10.14429/djlit.39.4.14460.
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 The present study investigated the status and impact of social media and networking sites on College of Medicine Nursing and Health Sciences’ students of Fiji National University, Fiji. Likert scale was used in the questionnaire. The collected data from 516 (86.00 per cent) usable questionnaires was tabulated and analysed using statistical tools and techniques. The findings showed that the majority of students participated in and satisfied with high usage of Facebook, YouTube, and Instagram accessed through laptops and PCs on daily and weekly basis. The students made their profiles visible only for the well-known people and comforted with notorious postings. The positive impacts as communication with family and friends, participation in networking activities, and involvement in social activities, as well as negative impacts as discontinuation to the sites for misusing their information, distraction from research/assignments/careers activities, continue if the account is hacked, no review of privacy settings for controlling notorious postings, and consume too much time were identified as the utmost effects of social media and SNSs. This study provides opportunity to higher management to review the social software for the benefit of Fiji National University and to carry out future related studies especially in Fiji.
 
 
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Pouchin, Pierre, Rayan Zoghlami, Rémi Valarcher, et al. "Easing batch image processing from OMERO: a new toolbox for ImageJ." F1000Research 11 (April 5, 2022): 392. http://dx.doi.org/10.12688/f1000research.110385.1.
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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 to analyse them. However, there is a lack of an easy-to-use generic tool to run a workflow on a batch of images without having to download them to local computers; and to automatically organize the results in OMERO. To offer this functionality, we have built three tools in Java language: “Simple OMERO Client”, a library to communicate with an OMERO database from Java softwares ; an ImageJ/Fiji plugin to run a macro-program on a batch of images from OMERO and “OMERO Macro extensions“, a dedicated vocabulary to interact with OMERO in macro-programming. The latter is intended for developers, with additional possibilities using tag criteria, while the “Batch OMERO plugin” is more geared towards non-IT scientists and has a very easy to use interface. Both tools are illustrated with a use case.
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Pouchin, Pierre, Rayan Zoghlami, Rémi Valarcher, et al. "Easing batch image processing from OMERO: a new toolbox for ImageJ." F1000Research 11 (September 12, 2022): 392. http://dx.doi.org/10.12688/f1000research.110385.2.
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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 to analyse them. However, there is a lack of an easy-to-use generic tool to run a workflow on a batch of images without having to download them to local computers, and to automatically organize the results in OMERO. To offer this functionality, we have built (i) a library in Java: “Simple OMERO Client”, to communicate with an OMERO database from Java software, (ii) an ImageJ/Fiji plugin to run a macro-program on a batch of images from OMERO and (iii) a new set of Macro Functions, “OMERO Macro extensions“, dedicated to interact with OMERO in macro-programming. The latter is intended for developers, with additional possibilities using tag criteria, while the “Batch OMERO plugin” is more geared towards non-IT scientists and has a very easy to use interface. Each tool is illustrated with a use case.
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Nunez-Iglesias, Juan, Adam J. Blanch, Oliver Looker, Matthew W. Dixon, and Leann Tilley. "A new Python library to analyse skeleton images confirms malaria parasite remodelling of the red blood cell membrane skeleton." PeerJ 6 (February 15, 2018): e4312. http://dx.doi.org/10.7717/peerj.4312.
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We present Skan (Skeleton analysis), a Python library for the analysis of the skeleton structures of objects. It was inspired by the “analyse skeletons” plugin for the Fiji image analysis software, but its extensive Application Programming Interface (API) allows users to examine and manipulate any intermediate data structures produced during the analysis. Further, its use of common Python data structures such as SciPy sparse matrices and pandas data frames opens the results to analysis within the extensive ecosystem of scientific libraries available in Python. We demonstrate the validity of Skan’s measurements by comparing its output to the established Analyze Skeletons Fiji plugin, and, with a new scanning electron microscopy (SEM)-based method, we confirm that the malaria parasite Plasmodium falciparum remodels the host red blood cell cytoskeleton, increasing the average distance between spectrin-actin junctions.
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Pooja I Shettannavar, Dishitha Kopoori, Vivek Chail, and Vasudha Kulkarni. "Fractal Analysis of Chest Radiographs Using Image-J-FIJI Software- A Pilot Study." International Journal of Anatomy and Research 12, no. 4 (2024): 9085–92. https://doi.org/10.16965/ijar.2024.237.
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Background: Lung vasculature has nutritive and functional roles. Unlike the bronchial tree which branches dichotomously into twenty-one generations, the pulmonary arteries give supernumerary branches to perfuse the neighboring parenchyma. The pulmonary arteries additionally branch for five more generations than airways before forming capillaries. Further pulmonary veins are interlobular in position. Hence the characterization quantifying the pulmonary vascular networks is challenging. Objective: In this study, we assessed the pulmonary vasculature in chest radiographs using the fractal analysis method on Image-J-Fiji software. Design: Cross-sectional study Settings: Patients referred to the Department of Radiodiagnosis, Akash Institute of Medical Sciences and Research Centre and Dr. B. R. Ambedkar Medical College, Bangalore, Karnataka, India Participants: One hundred and thirty-two chest radiographs of normal healthy individuals (aged 2 months to 80 years) were photographed. Each of these images was processed in the Image-J-Fiji software. A box-counting algorithm quantified the images. Data results of the fractal dimensions were validated at the probability of significance [0.05]. Results: The mean fractal dimension of the pulmonary vasculature was 1.39. For males and females, the Pearson's correlation coefficient between the fractal dimension and age in years was 0.102 and 0.16, respectively. In males, a chi-square value of 0.58, in females, a chi-square value of 1.03, degree of freedom 2 and critical value of p-value 0.05, showed the relation was statistically not significant. Comparison between fractal dimension and Gender using Cramer’s V test in males, 0.066, and in females, 0.088, indicates a weak association between fractal dimension and gender. Conclusion: The applicability of the fractal dimensions is to screen the high risks of severe chronic obstructive pulmonary diseases. The determination of fractal values helps evaluate the complexity of lung tumors. The baseline data concerning fractal properties of pulmonary vasculature obtained from this study helps to evaluate lung diseases like emphysema and vascular abnormalities during the progression of chronic obstructive pulmonary disease. KEYWORDS: Chest Radiograph, Image Analysis, Fractal dimension, Pulmonary vasculature.
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Kumar, Bimal Aklesh. "Improving Performance and Scalability of Fiji National University Campus Information System Using N-Tier Architecture." International Journal of Distributed Systems and Technologies 4, no. 2 (2013): 51–66. http://dx.doi.org/10.4018/jdst.2013040104.
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Software architecture is very important in the development of large scale software solution and plays a very active role in achieving business goals. This research is an attempt to utilize the N-Tier software architecture for developing a prototype campus information system for Fiji National University (FNU-CIS), to address the issue of performance and scalability. To assist in the design and implementation of FNU-CIS, an extensive evaluation of campus information systems is carried out to provide the bench mark on the current technology. FNU-CIS software architecture is designed with the implementation using JEE and CORBA. Experiments were carried out to assess the performance and scalability of the newly developed system. Several tests were carried out to measure the response time, throughput and latency of our system in distributed settings, and the results mainly favored FNU-CIS. This research makes a significant contribution to the field of software engineering in today’s world where performance and scalability of IT applications are often equated with better business, the process and techniques used in building such systems is paramount. The ideas presented in this paper can be easily utilized for the development of other large scale systems with similar issues such as performance and scalability to be addressed.
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Odrovakavula, Latileta, and Masoud Mohammadnezhad. "Exploring Physical and Social Wellness of High School Students in Suva, Fiji." Global Journal of Health Science 14, no. 2 (2021): 8. http://dx.doi.org/10.5539/gjhs.v14n2p8.
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BACKGROUND: Given the characteristics of the adolescence life stage, the physical and social wellness dimensions remain a challenge. The aim of this study was to determine adolescent perceptions of physical and social wellness in secondary schools in Fiji. 
 
 MATERIALS & METHODS: Four purposively selected secondary schools in Suva, Fiji were part of this qualitative cross sectional study in 2019. Fijian students enrolled into years 11 to 13 in the selected schools were invited to participate. Participants were purposively sampled. Data was collected using a structured self-administered questionnaire. Descriptive statistics were generated through the Statistical Package for the Social Sciences software version 25. 
 
 RESULTS: A total of 350 high school students, with the mean age of 17.5 (SD = ±0.9), participated in the study. The majority (48%) had very high scores for physical wellness and a fifth of the participants (28%) had low scores. In terms of social wellness, about a third (28.9%) scored low whilst the majority (40.3%) had high scores of social wellness. 
 
 CONCLUSION: This study adds to the pool of knowledge for wellness increases chances of improvement in adolescent program development specifically in terms of physical and social wellness. Appropriate interventions are recommended to improve physical and social wellness in high school students in Fiji.
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Out, Welmoed A., José F. Pertusa Grau, and Marco Madella. "A New Method for Morphometric Analysis of Opal Phytoliths from Plants." Microscopy and Microanalysis 20, no. 6 (2014): 1876–87. http://dx.doi.org/10.1017/s1431927614013270.
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AbstractMicro-morphometry has substantially gained ground in the field of phytolith analysis, but the comparability of results is limited due to the use of different methods. This paper presents a new, user-friendly method based on open-source software (FIJI) that is proposed as a step towards the introduction of a standard method. After obtaining a mask of a phytolith by making a digital drawing, 27 commonly used variables of size and shape are measured automatically. This method is not only useful for phytolith analysis, but may also be used for other fields of morphometric research. Users can furthermore customize the software tool when additional variables are required.
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Encarnacion-Rivera, Lucas, Steven Foltz, H. Criss Hartzell, and Hyojung Choo. "Myosoft: An automated muscle histology analysis tool using machine learning algorithm utilizing FIJI/ImageJ software." PLOS ONE 15, no. 3 (2020): e0229041. http://dx.doi.org/10.1371/journal.pone.0229041.
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Bijelić, Nikola, Tatjana Belovari, Dunja Stolnik, Ivana Lovrić, and Mirela Baus Lončar. "Histomorphometric Parameters of the Growth Plate and Trabecular Bone in Wild-Type and Trefoil Factor Family 3 (Tff3)-Deficient Mice Analyzed by Free and Open-Source Image Processing Software." Microscopy and Microanalysis 23, no. 4 (2017): 818–25. http://dx.doi.org/10.1017/s1431927617000630.
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AbstractTrefoil factor family 3 (Tff3) peptide is present during intrauterine endochondral ossification in mice, and its deficiency affects cancellous bone quality in secondary ossification centers of mouse tibiae. The aim of this study was to quantitatively analyze parameters describing the growth plate and primary ossification centers in tibiae of 1-month-old wild-type and Tff3 knock-out mice (n=5 per genotype) by using free and open-source software. Digital photographs of the growth plates and trabecular bone were processed by open-source computer programs GIMP and FIJI. Histomorphometric parameters were calculated using measurements made with FIJI. Tff3 knock-out mice had significantly smaller trabecular number and significantly larger trabecular separation. Trabecular bone volume, trabecular bone surface, and trabecular thickness showed no significant difference between the two groups. Although such histomorphological differences were found in the cancellous bone structure, no significant differences were found in the epiphyseal plate histomorphology. Tff3 peptide probably has an effect on the formation and quality of the cancellous bone in the primary ossification centers, but not through disrupting the epiphyseal plate morphology. This work emphasizes the benefits of using free and open-source programs for morphological studies in life sciences.
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Sadikan, Muhammad Zulfiqah, Nurul Alimah Abdul Nasir, Nurliyana Ain Abdul Ghani, Lidawani Lambuk, Igor Nikolayevich Iezhitsa, and And Renu Agarwal. "The Use of Fiji Image J as an Image Analysis Tool for Measuring Retinal Vessel Diameter in Rodent Model of Diabetic Retinopathy." Asian Journal of Medicine and Biomedicine 5, no. 1 (2021): 61–66. http://dx.doi.org/10.37231/ajmb.2021.5.1.422.
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The purpose of this study was to evaluate the use of Fiji Image J application for digital fundus image analysis of retinal vessel diameter in diabetic retinopathy rat model. Male Sprague-Dawley rats, weighing 200-250 grams, were divided into two groups: normal and diabetic. The diabetes was induced by intraperitoneal (IP) injection of streptozotocin (STZ, 55 mg/kg body weight). Normal rats received IP citrate buffer. Fundus images were captured at week 0, 6 and 12 post-induction to observe changes in retinal veins and arteries. Images obtained were then analyzed using Fiji Image J software. Retinal venous diameter was increased in both groups at week 6 and 12 compared to baseline (p<0.05). However, no significant differences were seen in the retinal venous diameter at week 12 compared to week 6 in both groups. When comparing between the groups, retinal venous diameter in diabetic group was significantly greater compared to normal group at week 6 and 12 by 1.37- and 1.35-folds (p<0.001), respectively. For the retinal arterial diameter in diabetic group, an increase was observed at week 6 and 12 compared to baseline by 1.17- and 1.2-folds (p<0.05) respectively, however, similar changes were not observed in normal group. There was also no significant difference between the retinal arterial diameter of normal and diabetic group at week 6 and 12. In conclusion, retinal vessels diameter analysis of fundus images using Fiji Image J can be utilized to determine quantitative changes between normal and rats with STZ-induced diabetic retinopathy.
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Wieland, Fredrik, Anika Schumacher, Nadia Roumans, Clemens van Blitterswijk, Vanessa LaPointe, and Timo Rademakers. "Methodological approaches in aggregate formation and microscopic analysis to assess pseudoislet morphology and cellular interactions." Open Research Europe 2 (July 13, 2022): 87. http://dx.doi.org/10.12688/openreseurope.14894.1.
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Microscopy has revolutionised our view on biology and has been vital for many discoveries since its invention around 200 years ago. Recent developments in cell biology have led to a strong interest in generating spheroids and organoids that better represent tissue. However, the current challenge faced by many researchers is the culture and analysis of these three-dimensional (3D) cell cultures. With the technological improvements in reconstructing volumetric datasets by optical sections, it is possible to quantify cells, their spatial arrangement, and the protein distribution without destroying the physical organization. We assessed three different microwell culture plates and four analysis tools for 3D imaging data for their applicability for the analysis of 3D cultures. A key advantage of microwell plates is their potential to perform high-throughput experiments in which cell cultures are generated and analysed in one single system. However, it was shown that this potential could be impacted by the material composition and microwell structure. For example, antibody staining was not possible in a hydrogel microwell, and truncated pyramid–structured microwells had increased background fluorescence due to their structure. Regarding analysis tools, four different software, namely CellProfiler, Fiji/ImageJ, Nikon GA3 and Imaris, were compared for their accuracy and applicability in analysing datasets from 3D cultures. The results showed that the open-access software, CellProfiler and Fiji, could quantify nuclei and cells, yet with varying results compared to manual counting, and may require post-processing optimisation. On the other hand, the GA3 and Imaris software packages showed excellent versatility in usage and accuracy in the quantification of nuclei and cells, and could classify cell localisation. Together these results provide critical considerations for microscopic imaging and analysis of 3D cell cultures.
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Wieland, Fredrik, Anika Schumacher, Nadia Roumans, Clemens van Blitterswijk, Vanessa LaPointe, and Timo Rademakers. "Methodological approaches in aggregate formation and microscopic analysis to assess pseudoislet morphology and cellular interactions." Open Research Europe 2 (September 20, 2022): 87. http://dx.doi.org/10.12688/openreseurope.14894.2.
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Microscopy has revolutionised our view on biology and has been vital for many discoveries since its invention around 200 years ago. Recent developments in cell biology have led to a strong interest in generating spheroids and organoids that better represent tissue. However, the current challenge faced by many researchers is the culture and analysis of these three-dimensional (3D) cell cultures. With the technological improvements in reconstructing volumetric datasets by optical sections, it is possible to quantify cells, their spatial arrangement, and the protein distribution without destroying the physical organization. We assessed three different microwell culture plates and four analysis tools for 3D imaging data for their applicability for the analysis of 3D cultures. A key advantage of microwell plates is their potential to perform high-throughput experiments in which cell cultures are generated and analysed in one single system. However, it was shown that this potential could be impacted by the material composition and microwell structure. For example, antibody staining was not possible in a hydrogel microwell, and truncated pyramid–structured microwells had increased background fluorescence due to their structure. Regarding analysis tools, four different software, namely CellProfiler, Fiji/ImageJ, Nikon GA3 and Imaris, were compared for their accuracy and applicability in analysing datasets from 3D cultures. The results showed that the open-access software, CellProfiler and Fiji, could quantify nuclei and cells, yet with varying results compared to manual counting, and may require post-processing optimisation. On the other hand, the GA3 and Imaris software packages showed excellent versatility in usage and accuracy in the quantification of nuclei and cells, and could classify cell localisation. Together these results provide critical considerations for microscopic imaging and analysis of 3D cell cultures.
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Čapek, Martin, Michaela Blažíková, Ivan Novotný, et al. "The Wavelet-Based Denoising Of Images in Fiji, With Example Applications in Structured Illumination Microscopy." Image Analysis & Stereology 40, no. 1 (2021): 3–16. http://dx.doi.org/10.5566/ias.2432.
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Filtration of super-resolved microscopic images brings often troubles with removing undesired image parts like, e.g., noise, inhomogenous background and reconstruction artifacts. Standard filtration techniques, e.g., convolution- or Fourier transform-based methods are not always appropriate, since they may lower image resolution that was acquired by hi-tech and expensive microscopy systems. Thus, in this article it is proposed to filter such images using discrete wavelet transform (DWT). Newly developed Wavelet_Denoise plugin for free available Fiji software package demonstrates important possibilities of applying DWT to images: Decomposition of a filtered picture using various wavelet filters and levels of details with showing decomposed images and visualization of effects of back transformation of the picture with chosen level of suppression or denoising of wavelet coefficients. The Fiji framework allows, for example, using a plethora of various microscopic image formats for data opening, users can easily install the plugin through a menu command and the plugin supports processing 3D images in Z-stacks. The application of the plugin for removal of reconstruction artifacts and undesirable background in images acquired by super-resolved structured illumination microscopy is demonstrated as well.
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Khodanovich, Marina Y., Tatyana V. Anan’ina, Elena P. Krutenkova, et al. "Challenges and Practical Solutions to MRI and Histology Matching and Measurements Using Available ImageJ Software Tools." Biomedicines 10, no. 7 (2022): 1556. http://dx.doi.org/10.3390/biomedicines10071556.
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Traditionally histology is the gold standard for the validation of imaging experiments. Matching imaging slices and histological sections and the precise outlining of corresponding tissue structures are difficult. Challenges are based on differences in imaging and histological slice thickness as well as tissue shrinkage and alterations after processing. Here we describe step-by-step instructions that might be used as a universal pathway to overlay MRI and histological images and for a correlation of measurements between imaging modalities. The free available (Fiji is just) ImageJ software tools were used for regions of interest transformation (ROIT) and alignment using a rat brain MRI as an example. The developed ROIT procedure was compared to a manual delineation of rat brain structures. The ROIT plugin was developed for ImageJ to enable an automatization of the image processing and structural analysis of the rodent brain.
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McMichael, Celia, and Teresia Powell. "Planned Relocation and Health: A Case Study from Fiji." International Journal of Environmental Research and Public Health 18, no. 8 (2021): 4355. http://dx.doi.org/10.3390/ijerph18084355.
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In Fiji, low-lying coastal villages are beginning to retreat and relocate in response to coastal erosion, flooding and saltwater intrusion. Planned relocation is considered a last resort as a form of adaptation to the impacts of climatic and environmental change. The health impacts of planned relocation are poorly understood. This paper draws on data from multi-year research with residents of the iTaukei (Indigenous) Fijian village of Vunidogoloa. We used qualitative research methods to examine experiences of planned relocation, including residents’ accounts of their health and quality of life. In-depth interviews and group discussions were conducted with villagers living in a site of relocation, at four points in time (2015, 2016, 2019, and 2020). Twenty-seven people in Vunidogoloa, Fiji, participated in in-depth interviews, several on more than one occasion. Six group discussions with between eight to twelve participants were also conducted. Qualitative analytic software (NVivo) was used to analyse interview transcripts and identify themes. Villagers report both health benefits and challenges following planned relocation. Key facilitators for good health include movement away from some environmental risks to health, adequate drinking water and sanitation, food security including through farms and kitchen gardens, livelihood opportunities, improved access to schools and health services, and appropriate housing design. However, residents also refer to unanticipated risks to health including increased consumption of packaged goods and alcohol, disruptions to social structures and traditional values, and disrupted place attachment following movement away from a coastal site of belonging with consequences for mental wellbeing. Therefore, planned relocation has altered the social determinants of health in complex ways, bringing both health opportunities and risks. These results highlight the need for context-specific planning and adaptation programs that include meaningful involvement of community members in ongoing decision making, and call for an understanding of diverse social determinants of health that emerge and evolve in contexts of planned relocation.
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Hossain, Md Amjad, Preoyati Khan, Cheng Chang Lu, and Robert J. Clements. "Distributed ImageJ(Fiji): a framework for parallel image processing." IET Image Processing 14, no. 12 (2020): 2937–47. http://dx.doi.org/10.1049/iet-ipr.2019.0150.
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Maharaj, Ronald, Sushil Kumar, Nicholas Rollings, and Andreas Antoniou. "Groundwater Detection Using Resistivity at Nubutautau Village in Viti Levu in Fiji." Water 15, no. 23 (2023): 4156. http://dx.doi.org/10.3390/w15234156.
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A geophysical method, electrical resistivity tomography, was applied to identify potential groundwater-bearing zones around Nubutautau village on Viti Levu island, Fiji. Apparent resistivity data of the subsurface were collected through an electrode assembly along survey lines by injecting current into the subsurface using an ABEM Terrameter LS2. The apparent resistivity data were inverted using Res2DINVx64 software to produce the final electrical resistivity through an iterative process to compare the resistivity of layers and draw analogical hydrogeological results. Analysis revealed the presence of two potential groundwater-bearing zones as potential targets for future drilling. The two targets indicated the presence of potentially saturated vertical fractures through which infiltrating rainwater percolates through the volcanic rock towards a deeper basal aquifer. The identification of the two potential targets demonstrated great potential of this geophysical technique to effectively inform drilling operations. A scientific approach can increase the successful delivery of water security interventions in remote, drought-prone communities of the Pacific.
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Fassina, Lorenzo, Maria Rita Assenza, Michele Miragoli, Andrea M. Isidori, Fabio Naro, and Federica Barbagallo. "Cell Shortening and Calcium Homeostasis Analysis in Adult Cardiomyocytes via a New Software Tool." Biomedicines 10, no. 3 (2022): 640. http://dx.doi.org/10.3390/biomedicines10030640.
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Intracellular calcium (Ca2+) is the central regulator of heart contractility. Indeed, it couples the electrical signal, which pervades the myocardium, with cardiomyocytes contraction. Moreover, alterations in calcium management are the main factors contributing to the mechanical and electrical dysfunction observed in failing hearts. So, simultaneous analysis of the contractile function and intracellular Ca2+ is indispensable to evaluate cardiomyocytes activity. Intracellular Ca2+ variations and fraction shortening are commonly studied with fluorescent Ca2+ indicator dyes associated with microscopy techniques. However, tracking and dealing with multiple files manually is time-consuming and error-prone and often requires expensive apparatus and software. Here, we announce a new, user-friendly image processing and analysis tool, based on ImageJ-Fiji/MATLAB® software, to evaluate the major cardiomyocyte functional parameters. We succeeded in analyzing fractional cell shortening, Ca2+ transient amplitude, and the kinematics/dynamics parameters of mouse isolated adult cardiomyocytes. The proposed method can be applied to evaluate changes in the Ca2+ cycle and contractile behavior in genetically or pharmacologically induced disease models, in drug screening and other common applications to assess mammalian cardiomyocyte functions.
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Pramana, A. A., G. Riantomo, A. P. Oktaviani, I. Setiabudi, F. D. E. Latief, and M. A. Gibrata. "Digital Rock Physics Application in Determining The Porosity of Shale Rock." Journal of Physics: Conference Series 2243, no. 1 (2022): 012021. http://dx.doi.org/10.1088/1742-6596/2243/1/012021.
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Abstract This research is focusing on determining the porosity of shale rock using the Digital Rock Physics (DRP) method. The DRP method uses fiji software to process μCT-scan data of shale coreplug through segmentation and thresholding processes to determine the pores of the rock and then to determine the value of rock porosity. The purpose of this research is to be able to determine the value of rock porosity more quickly and to verify the DRP porosity result to that of laboratory test. The result shows that the porosity value obtained by the DRP method and laboratory test has a small difference so that the DRP method is quite reliable.
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Čepa, Martin. "Segmentation of Total Cell Area in Brightfield Microscopy Images." Methods and Protocols 1, no. 4 (2018): 43. http://dx.doi.org/10.3390/mps1040043.
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Segmentation is one of the most important steps in microscopy image analysis. Unfortunately, most of the methods use fluorescence images for this task, which is not suitable for analysis that requires a knowledge of area occupied by cells and an experimental design that does not allow necessary labeling. In this protocol, we present a simple method, based on edge detection and morphological operations, that separates total area occupied by cells from the background using only brightfield channel image. The resulting segmented picture can be further used as a mask for fluorescence quantification and other analyses. The whole procedure is carried out in open source software Fiji.
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Ahammer, Helmut, Martin A. Reiss, Moritz Hackhofer, et al. "ComsystanJ: A collection of Fiji/ImageJ2 plugins for nonlinear and complexity analysis in 1D, 2D and 3D." PLOS ONE 18, no. 10 (2023): e0292217. http://dx.doi.org/10.1371/journal.pone.0292217.
Full textAbstract:
Complex systems such as the global climate, biological organisms, civilisation, technical or social networks exhibit diverse behaviours at various temporal and spatial scales, often characterized by nonlinearity, feedback loops, and emergence. These systems can be characterized by physical quantities such as entropy, information, chaoticity or fractality rather than classical quantities such as time, velocity, energy or temperature. The drawback of these complexity quantities is that their definitions are not always mathematically exact and computational algorithms provide estimates rather than exact values. Typically, evaluations can be cumbersome, necessitating specialized tools. We are therefore introducing ComsystanJ, a novel and user-friendly software suite, providing a comprehensive set of plugins for complex systems analysis, without the need for prior programming knowledge. It is platform independent, end-user friendly and extensible. ComsystanJ combines already known algorithms and newer methods for generalizable analysis of 1D signals, 2D images and 3D volume data including the generation of data sets such as signals and images for testing purposes. It is based on the framework of the open-source image processing software Fiji and ImageJ2. ComsystanJ plugins are macro recordable and are maintained as open-source software. ComsystanJ includes effective surrogate analysis in all dimensions to validate the features calculated by the different algorithms. Future enhancements of the project will include the implementation of parallel computing for image stacks and volumes and the integration of artificial intelligence methods to improve feature recognition and parameter calculation.
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Ahammer, Helmut, Martin A. Reiss, Moritz Hackhofer, et al. "ComsystanJ: A collection of Fiji/ImageJ2 plugins for nonlinear and complexity analysis in 1D, 2D and 3D." PloS One 18, no. 10 (2023): e0292217. https://doi.org/10.1371/journal.pone.0292217.
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<strong>Abstract:</strong> Complex systems such as the global climate, biological organisms, civilisation, technical or social networks exhibit diverse behaviours at various temporal and spatial scales, often characterized by nonlinearity, feedback loops, and emergence. These systems can be characterized by physical quantities such as entropy, information, chaoticity or fractality rather than classical quantities such as time, velocity, energy or temperature. The drawback of these complexity quantities is that their definitions are not always mathematically exact and computational algorithms provide estimates rather than exact values. Typically, evaluations can be cumbersome, necessitating specialized tools. We are therefore introducing ComsystanJ, a novel and user-friendly software suite, providing a comprehensive set of plugins for complex systems analysis, without the need for prior programming knowledge. It is platform independent, end-user friendly and extensible. ComsystanJ combines already known algorithms and newer methods for generalizable analysis of 1D signals, 2D images and 3D volume data including the generation of data sets such as signals and images for testing purposes. It is based on the framework of the open-source image processing software Fiji and ImageJ2. ComsystanJ plugins are macro recordable and are maintained as open-source software. ComsystanJ includes effective surrogate analysis in all dimensions to validate the features calculated by the different algorithms. Future enhancements of the project will include the implementation of parallel computing for image stacks and volumes and the integration of artificial intelligence methods to improve feature recognition and parameter calculation.
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Shiva, Amruthavakkula, Vignesh T. Sai, Subramaniyan V. Siva, Kumar T. Rajamani, and Sankara Sai S. Siva. "Development of an Interactive GUI Tool for Thyroid Uptake Studies using Gamma Camera." International Journal of Biomedical and Clinical Engineering 5, no. 1 (2016): 1–8. http://dx.doi.org/10.4018/ijbce.2016010101.
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Thyroid uptake study is a technique that requires injection of a radio-isotope/radiotracer emitting gamma rays into the blood stream of the patient to study the functionality of thyroid in accordance to its uptake. The Gamma Camera uses a LEAP (Low Energy All Purpose) collimator which handles only photons emitted from radio-isotopes having lower emission energies. Technetium-99m is used whose energy of emission is around 140 keV. For a typical Thyroid Uptake Probe where Iodine-131 having greater emission energy of 364 keV is preferred, but existing Thyroid Uptake software is not feasible. Therefore an Interactive GUI (Graphical User Interface) tool was developed using Fiji for determination of tracer uptake by manually drawing the Region of Interest around left and right thyroid lobes separately. Developed tool was tested on 35 real time thyroid cases and the uptake values obtained are compared with those obtained from the existing software tool.
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HAASE, M., O. GARGOMINY, and B. FONTAINE. "Rissooidean freshwater gastropods from the middle of the Pacific: the genus Fluviopupa on the Austral Islands (Caenogastropoda)." Molluscan Research 25, no. 3 (2005): 145–63. http://dx.doi.org/10.11646/mr.25.3.3.
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The Austral Islands comprising five islands of volcanic origin situated in the south of Polynesia, harbour what is probably the most isolated fauna of hydrobioid gastropods. To date, only two species belonging to the genus Fluviopupa have been known. We describe an additional four species. Each species is exclusive to one island. Two species each occur on Rapa and Raivavae. Only on the western-most, oldest, and most degraded island, Rimatara, were no hydrobioids found. The closest relatives occur on Fiji. Since no hydrobioids are known from the island groups between Fiji and the Austral Islands, viz. Tonga, Samoa and the Cook Islands, we assume that the common ancestor has arrived directly from Fiji before these islands were formed in the late Miocene, possibly transported by a bird. Four of the Austral species meet the IUCN criteria for Vulnerable while F. jeanyvesi n. sp. and F. tubuaia n. sp. are considered Critically Endangered. Both are known from a single locality on Raivavae and Tubuai, respectively, and they are threatened by habitat loss.
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Kugler, Elisabeth, Karen Plant, Timothy Chico, and Paul Armitage. "Enhancement and Segmentation Workflow for the Developing Zebrafish Vasculature." Journal of Imaging 5, no. 1 (2019): 14. http://dx.doi.org/10.3390/jimaging5010014.
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Zebrafish have become an established in vivo vertebrate model to study cardiovascular development and disease. However, most published studies of the zebrafish vascular architecture rely on subjective visual assessment, rather than objective quantification. In this paper, we used state-of-the-art light sheet fluorescence microscopy to visualize the vasculature in transgenic fluorescent reporter zebrafish. Analysis of image quality, vascular enhancement methods, and segmentation approaches were performed in the framework of the open-source software Fiji to allow dissemination and reproducibility. Here, we build on a previously developed image processing pipeline; evaluate its applicability to a wider range of data; apply and evaluate an alternative vascular enhancement method; and, finally, suggest a work-flow for successful segmentation of the embryonic zebrafish vasculature.
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Prasad, Rajneel Ravinesh. "Impact of Advanced Technologies on the Accounting Sector in Developing Nation: Evidence from Fiji." African Journal of Economics and Sustainable Development 6, no. 4 (2023): 126–33. http://dx.doi.org/10.52589/ajesd-kt7kiog3.
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The emergence of advanced technologies (blockchains, machine learning, data mining, cloud computing) in Fiji’s accounting sector have revolutionized how accounting works. It has increased data accuracy, human efficiency, enhanced real time data exchange and risk management and reduced costs. However, there have also been some negative impacts such as redundancy of basic accounting roles, increased data security threats, increased set up and training costs. This study examines the positive and negative impacts of adoption of new technologies by the accounting industry in Fiji and puts forward some recommendations on how these challenges could be effectively addressed so that, rather than being perceived as a threat, humans’ partner with these software and tools to reap the maximum benefits. Practical Contribution: The findings help stakeholders to implement effective business strategies to enhance positive impacts and mitigate negative impacts of advanced technologies especially in developing nations. Theoretical Contribution : This research contributes an empirical study to the literature on advanced technologies and accounting in developing nations.
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Schmied, Christopher, and Helena Klara Jambor. "Effective image visualization for publications – a workflow using open access tools and concepts." F1000Research 9 (February 18, 2021): 1373. http://dx.doi.org/10.12688/f1000research.27140.2.
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Today, 25% of figures in biomedical publications contain images of various types, e.g. photos, light or electron microscopy images, x-rays, or even sketches or drawings. Despite being widely used, published images may be ineffective or illegible since details are not visible, information is missing or they have been inappropriately processed. The vast majority of such imperfect images can be attributed to the lack of experience of the authors as undergraduate and graduate curricula lack courses on image acquisition, ethical processing, and visualization. Here we present a step-by-step image processing workflow for effective and ethical image presentation. The workflow is aimed to allow novice users with little or no prior experience in image processing to implement the essential steps towards publishing images. The workflow is based on the open source software Fiji, but its principles can be applied with other software packages. All image processing steps discussed here, and complementary suggestions for image presentation, are shown in an accessible “cheat sheet”-style format, enabling wide distribution, use, and adoption to more specific needs.
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Schmied, Christopher, and Helena Klara Jambor. "Effective image visualization for publications – a workflow using open access tools and concepts." F1000Research 9 (November 26, 2020): 1373. http://dx.doi.org/10.12688/f1000research.27140.1.
Full textAbstract:
Today, 25% of figures in biomedical publications contain images of various types, e.g. photos, light or electron microscopy images, x-rays, or even sketches or drawings. Despite being widely used, published images may be ineffective or illegible since details are not visible, information is missing or they have been inappropriately processed. The vast majority of such imperfect images can be attributed to the lack of experience of the authors as undergraduate and graduate curricula lack courses on image acquisition, ethical processing, and visualization. Here we present a step-by-step image processing workflow for effective and ethical image presentation. The workflow is aimed to allow novice users with little or no prior experience in image processing to implement the essential steps towards publishing images. The workflow is based on the open source software Fiji, but its principles can be applied with other software packages. All image processing steps discussed here, and complementary suggestions for image presentation, are shown in an accessible “cheat sheet”-style format, enabling wide distribution, use, and adoption to more specific needs.
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Dean, Mehwish, Ratu Osea Gavidi, Masoud Mohammadnezhad, and Richard D. Nair. "Prevalence and Characteristics of Oral Squamous Cell Carcinoma in Fiji: A Retrospective Study." Global Journal of Health Science 14, no. 3 (2022): 100. http://dx.doi.org/10.5539/gjhs.v14n3p100.
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BACKGROUND: Oral squamous cell carcinoma (OSCC) is malignant epithelial neoplasm that affects the oral cavity. Despite the large number of studies on OSCC in the literature, details on the demographic profile of these lesions in different populations are limited, especially amongst the Fijian population, thus this study aimed to determine the prevalence and characteristics of OSCC cases diagnosed from 2011 to 2015 at the Colonial War Memorial Hospital (CWMH), Suva, Fiji Islands. 
 
 MATERIALS &amp; METHODS: A retrospective quantitative study was carried out at the CWMH Histology department looking at OSCC cases diagnosed from 2011&ndash;2015. All confirmed cases were included in the study and excluded cases were suspected cases that were pending diagnosis and children. An extraction sheet was used for data collection which was designed to meet the requirements of study finding. This data was entered in SPSS software and then analyzed using the simple analytical tool as bar graphs and tables.&nbsp; 
 
 RESULTS: There were 74 OSCC cases diagnosed in the study period. The occurrence of OSCC cases over the 5-year period was fluctuant with the year 2013 recording the highest number of cases (24 cases, 32%). During the reported period, more men suffered (53 cases, 72%) from this condition with the tongue (40%) being the commonest oral cancer site followed by the lip and vermillion border (28%). Individuals in the 40 to 60 years&rsquo; age group (35 cases, 47.3%) were mostly affected with the I-taukei population (38 cases, 51.4%) recording the highest occurrence of OSCC. The results show that, the common occurrence is the tongue (40.5%) while the least presentation sight is Buccal mucosa/buccal sulcus area (8.1%). 
 
 CONCLUSION: The study concluded that more men suffer from oral squamous cell carcinoma compared to woman and the ethnicity that was most affected was I-taukei population. More detailed record keeping and reporting of oral cancer is needed to help evaluate progress in controlling oral cancer in the Fiji Islands. This availability of geographic data would further assist the Ministry of Health of Fiji in data collection and planning of preventative activities
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Caunce, S., D. Dadarwal, G. Adams, P. Brar, and J. Singh. "121 THREE-DIMENSIONAL ASSESSMENT OF EARLY CORPUS LUTEUM VASCULARITY IN BUFFALO (BUBALUS BUBALIS)." Reproduction, Fertility and Development 29, no. 1 (2017): 169. http://dx.doi.org/10.1071/rdv29n1ab121.
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The aim of the study was to develop an objective method to assess the vascular flow to the early corpus luteum (CL) in buffaloes using colour Doppler ultrasound data. Our hypothesis was that 3-dimensional (3D) volumetric analysis of vascularity would demonstrate lower variability between animals compared with conventional 2-dimensional (2D) analysis of single images. Wave emergence and ovulation was synchronized in buffalo (n = 16) using prostaglandin-GnRH based protocols. Colour Doppler ultrasonography (MyLab5, 7.5-MHz linear array, colour gain 65%) was performed daily from Day −2 to 4 (Day 0 = ovulation). Video clips of the ovaries (20 s at 18–28 frames per second, AVI) were recorded by slow and uniform free-hand movement of the transducer. Day 4 CL was used for analysis of vascular area and volume. For 2D vascularity assessment, 3 images (800 × 652 pixels, RGB, BMP) of each CL (at maximum apparent vascularity) were acquired through the clip image function on the ultrasound machine and analysed by ImageJ (Fiji) software (NIH, Bethesda, MD, USA). For 3D vascularity assessment, a portion of the video clip encompassing an entire ovary was identified and exported as a series of 2D TIFF images using Videomach software. The ultrasound scale bar was used to calculate the number of pixels per millimetre and to calibrate the X (horizontal) and Y (vertical) dimensions. For 2D analyses, the CL boundary was drawn using the free-hand manual selection tool in Fiji, the area of the CL (mm2) was recorded, and the border was then enlarged by 1.5 mm to include the peripheral vascular region of the CL. The colour threshold was adjusted to select the vascular region. The 2D vascularity score was calculated as the ratio of the coloured area to the enlarged luteal area. For 3D volumetric analyses, each series of TIFF images was imported as an image sequence in Fiji and colour thresholding (similar to 2D analysis) was applied to save a second TIFF series containing luteal vascular regions (coloured areas) only. The remaining volumetric analyses were completed in Imaris software using the ovarian volume (original TIFF series) and luteal vascular volume (second TIFF series) as separate channels. The Z-dimension thickness of each image was estimated by using the dimensions of a follicle within the same ovary (Z-axis diameter = mean diameter along X- and Y-axes). Similar to 2D analyses, the volume of the CL was obtained by drawing a border along the edge of the CL, the CL border was enlarged by 1.5 mm, and a 3D vascularity score was obtained by building a surface on the luteal vascular image and calculating the vascular to luteal volume ratio. The 2D vascularity score differed from 3D vascularity score (0.21 ± 0.02 v. 0.13 ± 0.02, paired t-test P < 0.01); however, variance did not differ (Bartlett’s test P = 0.32). Our initial results support the notion that the described technique of quantifying vascular volume of the corpus luteum may decrease the technical variability during image assessment and therefore better reflect the true vascularity compared with 2D image analyses. Research was supported by a grant from the Natural Sciences and Engineering Research Council of Canada.
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Scheible, Raphael. "GPU-Enabled Volume Renderer for Use with MATLAB." Digital 4, no. 4 (2024): 990–1007. https://doi.org/10.3390/digital4040049.
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Traditional tools, such as 3D Slicer, Fiji, and MATLAB®, often encounter limitations in rendering performance and data management as the dataset sizes increase. This work presents a GPU-enabled volume renderer with a MATLAB® interface that addresses these issues. The proposed renderer uses flexible memory management and leverages the GPU texture-mapping features of NVIDIA devices. It transfers data between the CPU and the GPU only in the case of a data change between renderings, and uses texture memory to make use of specific hardware benefits of the GPU and improve the quality. A case study using the ViBE-Z zebrafish larval dataset demonstrated the renderer’s ability to produce visualizations while managing extensive data effectively within the MATLAB® environment. The renderer is available as open-source software.
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Hasdiansah, Hasdiansah, Thala Viniolita Viniolita, Pristiansyah Pristiansyah, and Herianto Herianto. "OPTIMASI PARAMETER PROSES 3D PRINTING TERHADAP KELENGKUNGAN SOFT PNEUMATIC GRIPPER DENGAN MENGGUNAKAN FILAMENT EFLEX." Jurnal Rekayasa Mesin 15, no. 2 (2024): 685–92. http://dx.doi.org/10.21776/jrm.v15i2.1445.
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The emergence of 3D Printing technology has influenced several industries.3D Printing quickly produced mechanical components and prototype products with low production volumes. This research uses Cartesian DIY (Do It Yourself) 3D Printer and Eflex filament as material. This study aims to obtain the optimal process parameters set on the slicing software with the soft actuator angular response by giving two variations of 0.4 MPa and 0.6 MPa compressed air. Process parameters used in this study are flowrate, nozzle temperature, printing speed, and fan speed. This study aims to obtain the 3D printing process parameters using Fused Deposition Modeling (FDM) technology in producing soft actuators with the most optimal curvature angle using the Taguchi L9OA method. Measurement of soft actuator curvature angle using Fiji Image software. Based on the test results and the calculation of Taguchi analysis on the soft actuator curvature angle, the process parameter settings obtained in the slicing software for a pressure of 0.4 MPa are a flowrate of 105%, a nozzle temperature of 225 ºC, a printing speed of 30 mm/s, and a fan speed of 50%. Testing 0.6 MPa pressure is flowrate 105%, nozzle temperature 225 ºC, fan speed 50%, and printing speed 30 mm/s.
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Thuma, Tobin B. T., John A. Bogovic, Kammi B. Gunton, Hiram Jimenez, Bernardo Negreiros, and Jose S. Pulido. "The big warp: Registration of disparate retinal imaging modalities and an example overlay of ultrawide-field photos and en-face OCTA images." PLOS ONE 18, no. 4 (2023): e0284905. http://dx.doi.org/10.1371/journal.pone.0284905.
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Purpose To develop an algorithm and scripts to combine disparate multimodal imaging modalities and show its use by overlaying en-face optical coherence tomography angiography (OCTA) images and Optos ultra-widefield (UWF) retinal images using the Fiji (ImageJ) plugin BigWarp. Methods Optos UWF images and Heidelberg en-face OCTA images were collected from various patients as part of their routine care. En-face OCTA images were generated and ten (10) images at varying retinal depths were exported. The Fiji plugin BigWarp was used to transform the Optos UWF image onto the en-face OCTA image using matching reference points in the retinal vasculature surrounding the macula. The images were then overlayed and stacked to create a series of ten combined Optos UWF and en-face OCTA images of increasing retinal depths. The first algorithm was modified to include two scripts that automatically aligned all the en-face OCTA images. Results The Optos UWF image could easily be transformed to the en-face OCTA images using BigWarp with common vessel branch point landmarks in the vasculature. The resulting warped Optos image was then successfully superimposed onto the ten Optos UWF images. The scripts more easily allowed for automatic overlay of the images. Conclusions Optos UWF images can be successfully superimposed onto en-face OCTA images using freely available software that has been applied to ocular use. This synthesis of multimodal imaging may increase their potential diagnostic value. Script A is publicly available at https://doi.org/10.6084/m9.figshare.16879591.v1 and Script B is available at https://doi.org/10.6084/m9.figshare.17330048.
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Truckenbrodt, John, Terri Freemantle, Chris Williams, et al. "Towards Sentinel-1 SAR Analysis-Ready Data: A Best Practices Assessment on Preparing Backscatter Data for the Cube." Data 4, no. 3 (2019): 93. http://dx.doi.org/10.3390/data4030093.
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This study aims at assessing the feasibility of automatically producing analysis-ready radiometrically terrain-corrected (RTC) Synthetic Aperture Radar (SAR) gamma nought backscatter data for ingestion into a data cube for use in a large spatio-temporal data environment. As such, this study investigates the analysis readiness of different openly available digital elevation models (DEMs) and the capability of the software solutions SNAP and GAMMA in terms of overall usability as well as backscatter data quality. To achieve this, the study builds on the Python library pyroSAR for providing the workflow implementation test bed and provides a Jupyter notebook for transparency and future reproducibility of performed analyses. Two test sites were selected, over the Alps and Fiji, to be able to assess regional differences and support the establishment of the Swiss and Common Sensing Open Data cubes respectively.
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Abrougui, Khaoula, Nour El Houda Boughattas, Meriem Belhaj, et al. "Assessing Phytosanitary Application Efficiency of a Boom Sprayer Machine Using RGB Sensor in Grassy Fields." Sustainability 14, no. 6 (2022): 3666. http://dx.doi.org/10.3390/su14063666.
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The systematic use of plant protection products is now being called into question with the growing awareness of the risks they can represent for the environment and human health. The application of precision agriculture technologies helps to improve agricultural production but also to rationalize input costs and improve ecological footprints. Here we present a study on fungicide application efficiency and its impact on the grass quality of a golf course green using the free open-source image analysis software FIJI (Image J) to analyze ground RGB (high-resolution digital cameras) and multispectral aerial imagery in combination with experimental data of spray pressure and hydraulic slot nozzle size of a boom sprayer machine. The multivariate regression model best explained variance in the normalized green-red difference index (NGRDI) as a relevant indicator of healthy turfgrass fields from the aerial, ground, and machine data set.
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Pan, Yi Jun, Chien Kuo Yen, Feng Wei Cheng, Wen Hao Hsing, and Wei Sheng Chuang. "Uniformity of Nanofiber Alignment by Electrospinning." Advanced Materials Research 287-290 (July 2011): 2635–39. http://dx.doi.org/10.4028/www.scientific.net/amr.287-290.2635.
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Electrospinning of polyacrylonitrile was used to investigate the effect of horizontal vs. vertical fiber deposition methods and operating variables on the degree of nanofiber alignment. A high-speed camera and Fiji image analysis software were used to assess differences and changes in the degree of fiber parallelism, allowing for effective analysis of the impact of operating variables on fiber parallel alignment. The results show that the strength of the electric field affects the fibers to assume a parallel alignment. Too weak the electric field, the fibers are unable to form a straight bundle, but too strong a field results in chaotic fiber alignment. The distance between the collectors influences the angle distribution of the fiber parallel alignment greatly. Comparing the effect of horizontal and vertical electrospinning on fiber alignment shows that horizontal results in a more optimal degree of parallel fiber alignment.
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Nowak, Jacqueline, Kristin Gennermann, Staffan Persson, and Zoran Nikoloski. "CytoSeg 2.0: automated extraction of actin filaments." Bioinformatics 36, no. 9 (2020): 2950–51. http://dx.doi.org/10.1093/bioinformatics/btaa035.
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Abstract Motivation Actin filaments (AFs) are dynamic structures that substantially change their organization over time. The dynamic behavior and the relatively low signal-to-noise ratio during live-cell imaging have rendered the quantification of the actin organization a difficult task. Results We developed an automated image-based framework that extracts AFs from fluorescence microscopy images and represents them as networks, which are automatically analyzed to identify and compare biologically relevant features. Although the source code is freely available, we have now implemented the framework into a graphical user interface that can be installed as a Fiji plugin, thus enabling easy access by the research community. Availability and implementation CytoSeg 2.0 is open-source software under the GPL and is available on Github: https://github.com/jnowak90/CytoSeg2.0. Supplementary information Supplementary data are available at Bioinformatics online.
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Tero, Benjamin W., Bethany Fortier, Ashley N. Soucy, Ginger Paquette, and Lucy Liaw. "Quantification of Lipid Area within Thermogenic Mouse Perivascular Adipose Tissue Using Standardized Image Analysis in FIJI." Journal of Vascular Research 59, no. 1 (2021): 43–49. http://dx.doi.org/10.1159/000517178.
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Quantification of adipocyte size and number is routinely performed for white adipose tissues using existing image analysis software. However, thermogenic adipose tissue has multilocular adipocytes, making it difficult to distinguish adipocyte cell borders and to analyze lipid proportion using existing methods. We developed a simple, standardized method to quantify lipid content of mouse thermogenic adipose tissue. This method, using FIJI analysis of hematoxylin/eosin stained sections, was highly objective and highly reproducible, with ∼99% inter-rater reliability. The method was compared to direct lipid staining of adipose tissue, with comparable results. We used our method to analyze perivascular adipose tissue (PVAT) from C57BL/6 mice on a normal chow diet, compared to calorie restriction or a high fat diet, where lipid storage phenotypes are known. Results indicate that lipid content can be estimated within mouse PVAT in a quantitative and reproducible manner, and shows correlation with previously studied molecular and physiological measures.
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Teixeira, Felipe Pinheiro, Otávio da Fonseca Martins Gomes, and Flávio de Andrade Silva. "Degradation mechanisms of curaua, hemp, and sisal fibers exposed to elevated temperatures." BioResources 14, no. 1 (2019): 1494–511. http://dx.doi.org/10.15376/biores.14.1.1494-1511.
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The influence of elevated temperatures on mechanical behavior was studied for curaua, hemp, and sisal natural fibers. Tensile tests were performed on fibers heated at 100 °C, 150 °C, and 200 °C for 24 h, and reference samples were maintained without thermal treatment for comparisons. The cross sectional area of the fibers was measured using a scanning electron microscope (SEM), and the image analysis was performed using the open source software Fiji/ImageJ. These data allowed the computation of the tensile stresses and the correlation of the fiber morphology with its macro-mechanical behavior. The thermal degradation behavior of the natural fibers was measured via thermo-gravimetric analysis (TGA) and X-ray diffraction (XRD). The morphological and mechanical characteristics were described and discussed on a microstructural basis. The results showed that the loss of moisture leads to a significant increase in tensile strength before reaching the limits of the degradation range.
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Ségard, Bertrand-David, Kodai Kimura, Yuimi Matsuoka, Tomomi Imamura, Ayana Ikeda, and Takahiro Iwamiya. "Quantification of fibrosis extend and airspace availability in lung: A semi-automatic ImageJ/Fiji toolbox." PLOS ONE 19, no. 2 (2024): e0298015. http://dx.doi.org/10.1371/journal.pone.0298015.
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The evaluation of the structural integrity of mechanically dynamic organs such as lungs is critical for the diagnosis of numerous pathologies and the development of therapies. This task is classically performed by histology experts in a qualitative or semi-quantitative manner. Automatic digital image processing methods appeared in the last decades, and although immensely powerful, tools are highly specialized and lack the versatility required in various experimental designs. Here, a set of scripts for the image processing software ImageJ/Fiji to easily quantify fibrosis extend and alveolar airspace availability in Sirius Red or Masson’s trichrome stained samples is presented. The toolbox consists in thirteen modules: sample detection, particles filtration (automatic and manual), border definition, air ducts identification, air ducts walls definition, parenchyma extraction, MT-staining specific pre-processing, fibrosis detection, fibrosis particles filtration, airspace detection, and visualizations (tissue only or tissue and airspace). While the process is largely automated, critical parameters are accessible to the user for increased adaptability. The modularity of the protocol allows for its adjustment to alternative experimental settings. Fibrosis and airspace can be combined as an evaluation of the structural integrity of the organ. All settings and intermediate states are saved to ensure reproducibility. These new analysis scripts allow for a rapid quantification of fibrosis and airspace in a large variety of experimental settings.
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Hernández-Herrera, Paul, Yamel Ugartechea-Chirino, Héctor H. Torres-Martínez, et al. "Live Plant Cell Tracking: Fiji plugin to analyze cell proliferation dynamics and understand morphogenesis." Plant Physiology 188, no. 2 (2021): 846–60. http://dx.doi.org/10.1093/plphys/kiab530.
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Abstract Arabidopsis (Arabidopsis thaliana) primary and lateral roots (LRs) are well suited for 3D and 4D microscopy, and their development provides an ideal system for studying morphogenesis and cell proliferation dynamics. With fast-advancing microscopy techniques used for live-imaging, whole tissue data are increasingly available, yet present the great challenge of analyzing complex interactions within cell populations. We developed a plugin “Live Plant Cell Tracking” (LiPlaCeT) coupled to the publicly available ImageJ image analysis program and generated a pipeline that allows, with the aid of LiPlaCeT, 4D cell tracking and lineage analysis of populations of dividing and growing cells. The LiPlaCeT plugin contains ad hoc ergonomic curating tools, making it very simple to use for manual cell tracking, especially when the signal-to-noise ratio of images is low or variable in time or 3D space and when automated methods may fail. Performing time-lapse experiments and using cell-tracking data extracted with the assistance of LiPlaCeT, we accomplished deep analyses of cell proliferation and clonal relations in the whole developing LR primordia and constructed genealogical trees. We also used cell-tracking data for endodermis cells of the root apical meristem (RAM) and performed automated analyses of cell population dynamics using ParaView software (also publicly available). Using the RAM as an example, we also showed how LiPlaCeT can be used to generate information at the whole-tissue level regarding cell length, cell position, cell growth rate, cell displacement rate, and proliferation activity. The pipeline will be useful in live-imaging studies of roots and other plant organs to understand complex interactions within proliferating and growing cell populations. The plugin includes a step-by-step user manual and a dataset example that are available at https://www.ibt.unam.mx/documentos/diversos/LiPlaCeT.zip.
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Rahali, Rim, Yassine Ben Salem, Noura Dridi, and Hassen Dahman. "New foreground markers for Drosophila cell segmentation using marker-controlled watershed." International Journal of Electrical and Computer Engineering (IJECE) 12, no. 5 (2022): 5055. http://dx.doi.org/10.11591/ijece.v12i5.pp5055-5062.
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Image segmentation consists of partitioning the image into different objects of interest. For a biological image, the segmentation step is important to understand the biological process. However, it is a challenging task due to the presence of different dimensions for cells, intensity inhomogeneity, and clustered cells. The marker-controlled watershed (MCW) is proposed for segmentation, outperforming the classical watershed. Besides, the choice of markers for this algorithm is important and impacts the results. For this work, two foreground markers are proposed: kernels, constructed with the software Fiji and Obj.MPP markers, constructed with the framework Obj.MPP. The new proposed algorithms are compared to the basic MCW. Furthermore, we prove that Obj.MPP markers are better than kernels. Indeed, the Obj.MPP framework takes into account cell properties such as shape, radiometry, and local contrast. Segmentation results, using new markers and illustrated on real Drosophila dataset, confirm the good performance quality in terms of quantitative and qualitative evaluation.
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Blanco, Saúl, María Borrego-Ramos, and Adriana Olenici. "Disentangling diatom species complexes: does morphometry suffice?" PeerJ 5 (December 11, 2017): e4159. http://dx.doi.org/10.7717/peerj.4159.
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Accurate taxonomic resolution in light microscopy analyses of microalgae is essential to achieve high quality, comparable results in both floristic analyses and biomonitoring studies. A number of closely related diatom taxa have been detected to date co-occurring within benthic diatom assemblages, sharing many morphological, morphometrical and ecological characteristics. In this contribution, we analysed the hypothesis that, where a large sample size (number of individuals) is available, common morphometrical parameters (valve length, width and stria density) are sufficient to achieve a correct identification to the species level. We focused on some common diatom taxa belonging to the genusGomphonema. More than 400 valves and frustules were photographed in valve view and measured using Fiji software. Several statistical tools (mixture and discriminant analysis, k-means clustering, classification trees, etc.) were explored to test whether mere morphometry, independently of other valve features, leads to correct identifications, when compared to identifications made by experts. In view of the results obtained, morphometry-based determination in diatom taxonomy is discouraged.