computer-assisted image processing Dotaz Zobrazit nápovědu
For decades, biologists have relied on software to visualize and interpret imaging data. As techniques for acquiring images increase in complexity, resulting in larger multidimensional datasets, imaging software must adapt. ImageJ is an open-source image analysis software platform that has aided researchers with a variety of image analysis applications, driven mainly by engaged and collaborative user and developer communities. The close collaboration between programmers and users has resulted in adaptations to accommodate new challenges in image analysis that address the needs of ImageJ's diverse user base. ImageJ consists of many components, some relevant primarily for developers and a vast collection of user-centric plugins. It is available in many forms, including the widely used Fiji distribution. We refer to this entire ImageJ codebase and community as the ImageJ ecosystem. Here we review the core features of this ecosystem and highlight how ImageJ has responded to imaging technology advancements with new plugins and tools in recent years. These plugins and tools have been developed to address user needs in several areas such as visualization, segmentation, and tracking of biological entities in large, complex datasets. Moreover, new capabilities for deep learning are being added to ImageJ, reflecting a shift in the bioimage analysis community towards exploiting artificial intelligence. These new tools have been facilitated by profound architectural changes to the ImageJ core brought about by the ImageJ2 project. Therefore, we also discuss the contributions of ImageJ2 to enhancing multidimensional image processing and interoperability in the ImageJ ecosystem.
- Klíčová slova
- Fiji, ImageJ, image analysis, imaging, microscopy, open source software,
- MeSH
- počítačové zpracování obrazu * MeSH
- software * MeSH
- umělá inteligence * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
The digital polymerase chain reaction (dPCR) is an irreplaceable variant of PCR techniques due to its capacity for absolute quantification and detection of rare deoxyribonucleic acid (DNA) sequences in clinical samples. Image processing methods, including micro-chamber positioning and fluorescence analysis, determine the reliability of the dPCR results. However, typical methods demand high requirements for the chip structure, chip filling, and light intensity uniformity. This research developed an image-to-answer algorithm with single fluorescence image capture and known image-related error removal. We applied the Hough transform to identify partitions in the images of dPCR chips, the 2D Fourier transform to rotate the image, and the 3D projection transformation to locate and correct the positions of all partitions. We then calculated each partition's average fluorescence amplitudes and generated a 3D fluorescence intensity distribution map of the image. We subsequently corrected the fluorescence non-uniformity between partitions based on the map and achieved statistical results of partition fluorescence intensities. We validated the proposed algorithms using different contents of the target DNA. The proposed algorithm is independent of the dPCR chip structure damage and light intensity non-uniformity. It also provides a reliable alternative to analyze the results of chip-based dPCR systems.
- MeSH
- algoritmy MeSH
- DNA * genetika MeSH
- počítačové zpracování obrazu * MeSH
- polymerázová řetězová reakce MeSH
- reprodukovatelnost výsledků MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- DNA * MeSH
In this study, we examined different computer-assisted sperm analysis (CASA) systems (CRISMAS, Hobson Sperm Tracker, and Image J CASA) on the exact same video recordings to evaluate the differences in sperm motility parameters related to the specific CASA used. To cover a wide range of sperm motility parameters, we chose 12-second video recordings at 25 and 50 Hz frame rates after sperm motility activation using three taxonomically distinct fish species (sterlet: Acipenser ruthenus L.; common carp: Cyprinus carpio L.; and rainbow trout: Oncorhynchus mykiss Walbaum) that are characterized by essential differences in sperm behavior during motility. Systematically higher values of velocity and beat cross frequency (BCF) were observed in video recordings obtained at 50 Hz frame frequency compared with 25 Hz for all three systems. Motility parameters were affected by the CASA and species used for analyses. Image J and CRISMAS calculated higher curvilinear velocity (VCL) values for rainbow trout and common carp at 25 Hz frequency compared with the Hobson Sperm Tracker, whereas at 50 Hz, a significant difference was observed only for rainbow trout sperm recordings. No significant difference was observed between the CASA systems for sterlet sperm motility at 25 and 50 Hz. Additional analysis of 1-second segments taken at three time points (1, 6, and 12 seconds of the recording) revealed a dramatic decrease in common carp and rainbow trout sperm speed. The motility parameters of sterlet spermatozoa did not change significantly during the 12-second motility period and should be considered as a suitable model for longer motility analyses. Our results indicated that the CASA used can affect motility results even when the same motility recordings are used. These results could be critically altered by the recording quality, time of analysis, and frame rate of camera, and could result in erroneous conclusions.
- Klíčová slova
- CRISMAS, Fish spermatozoa, Hobson Sperm Tracker, Image J, Sperm velocity,
- MeSH
- analýza spermatu metody veterinární MeSH
- motilita spermií * MeSH
- počítačové zpracování obrazu přístrojové vybavení MeSH
- ryby * MeSH
- zvířata MeSH
- Check Tag
- mužské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- hodnotící studie MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
Cryo-electron microscopy has established as a mature structural biology technique to elucidate the three-dimensional structure of biological macromolecules. The Coulomb potential of the sample is imaged by an electron beam, and fast semi-conductor detectors produce movies of the sample under study. These movies have to be further processed by a whole pipeline of image-processing algorithms that produce the final structure of the macromolecule. In this chapter, we illustrate this whole processing pipeline putting in value the strength of "meta algorithms," which are the combination of several algorithms, each one with different mathematical rationale, in order to distinguish correctly from incorrectly estimated parameters. We show how this strategy leads to superior performance of the whole pipeline as well as more confident assessments about the reconstructed structures. The "meta algorithms" strategy is common to many fields and, in particular, it has provided excellent results in bioinformatics. We illustrate this combination using the workflow engine, Scipion.
- Klíčová slova
- Cryo-electron microscopy, Image processing, Scipion, Single particle,
- MeSH
- algoritmy * MeSH
- elektronová kryomikroskopie metody MeSH
- makromolekulární látky ultrastruktura MeSH
- molekulární biologie metody MeSH
- počítačové zpracování obrazu metody MeSH
- průběh práce MeSH
- výpočetní biologie MeSH
- zobrazení jednotlivé molekuly metody MeSH
- zobrazování trojrozměrné metody MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- makromolekulární látky MeSH
A software system STESYS for interactive and flexible generation of stereological test systems is described. STESYS enables to implement many of the recent unbiased stereological methods applied to biomedical research and clinical diagnosis by using a simple personal computer. Advantages of the STESYS software are illustrated by several examples of stereological measurements for estimating the number, total and mean cross-sectional area, volume and surface area.
This paper presents the most current and innovative solutions applying modern digital image processing methods for the purpose of skin cancer diagnostics. Skin cancer is one of the most common types of cancers. It is said that in the USA only, one in five people will develop skin cancer and this trend is constantly increasing. Implementation of new, non-invasive methods plays a crucial role in both identification and prevention of skin cancer occurrence. Early diagnosis and treatment are needed in order to decrease the number of deaths due to this disease. This paper also contains some information regarding the most common skin cancer types, mortality and epidemiological data for Poland, Europe, Canada and the USA. It also covers the most efficient and modern image recognition methods based on the artificial intelligence applied currently for diagnostics purposes. In this work, both professional, sophisticated as well as inexpensive solutions were presented. This paper is a review paper and covers the period of 2017 and 2022 when it comes to solutions and statistics. The authors decided to focus on the latest data, mostly due to the rapid technology development and increased number of new methods, which positively affects diagnosis and prognosis.
- Klíčová slova
- Data analysis, Diomedical engineering, Image processing, Skin cancer diagnostics,
- MeSH
- kůže MeSH
- lidé MeSH
- nádory kůže * diagnóza epidemiologie MeSH
- počítačové zpracování obrazu MeSH
- umělá inteligence * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
- Geografické názvy
- Kanada MeSH
PURPOSE: Breast ultrasonography (US) presents an alternative to mammography in young asymptomatic individuals and a complementary examination in screening of women with dense breasts. Handheld US is the standard-of-care, yet when used in whole-breast examination, no effort has been devoted to monitoring breast coverage and missed regions, which is the purpose of this study. METHODS: We introduce a computer-aided system assisting radiologists and US technologists in covering the whole breast with minimum alteration to the standard workflow. The proposed system comprises a standard US device, proprietary electromagnetic 3D tracking technology and software that combines US visual and tracking data to estimate a probe trajectory, total time spent in different breast segments, and a map of missed regions. A case study, which involved four radiologists (two junior and two senior) performing whole-breast ultrasound in 75 asymptomatic patients, was conducted to test the importance and relevance of the system. RESULTS: The mean process time per breast was [Formula: see text], with no statistically significant difference between the left and the right sides, and slightly longer examination time of junior radiologists. The process time density shows that central parts of the breast have better coverage compared to the periphery. Within the central part, missed regions of minimum detectable size of [Formula: see text] occur in [Formula: see text] of examinations, and non-negligible [Formula: see text] regions occur in [Formula: see text] of cases. CONCLUSION: The results of the case study indicate that missed regions are present in handheld whole-breast US, which renders the proposed system for tracking the probe position during examination a valuable tool for monitoring coverage.
- Klíčová slova
- Breast, Cancer, Coverage, Screening, Tracking, Ultrasound,
- MeSH
- design vybavení MeSH
- diagnóza počítačová * MeSH
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mamografie metody MeSH
- nádory prsu diagnostické zobrazování MeSH
- počítače do ruky MeSH
- počítačové systémy MeSH
- počítačové zpracování obrazu MeSH
- prsy diagnostické zobrazování MeSH
- reprodukovatelnost výsledků MeSH
- software MeSH
- ultrasonografie prsů metody MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- MeSH
- algoritmy * MeSH
- interpretace obrazu počítačem přístrojové vybavení metody MeSH
- lidé MeSH
- molekulární zobrazování metody MeSH
- počítačová grafika přístrojové vybavení trendy MeSH
- počítačové zpracování signálu přístrojové vybavení MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- dopisy MeSH
- práce podpořená grantem MeSH
The successful development of visualization techniques for live cell imaging leads to the development of suitable software for the acquisition and processing of multidimensional image data. This report compares several possible approaches to image acquisition and processing in confocal in vivo microscopy and suggests new alternatives to the published methods. Special attention is paid to spinning disk systems based either on a classical Nipkow disk or on the microlens principle. This study shows how to optimize image acquisition process in live cell studies using camera binning feature and how to perform object tracking using a new fast image registration method based on the graph theory.
- MeSH
- algoritmy MeSH
- fyziologie buňky * MeSH
- konfokální mikroskopie přístrojové vybavení MeSH
- luminescentní proteiny metabolismus MeSH
- obrazová cytometrie přístrojové vybavení metody MeSH
- počítačové zpracování obrazu metody MeSH
- software * MeSH
- zelené fluorescenční proteiny MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
- Názvy látek
- luminescentní proteiny MeSH
- zelené fluorescenční proteiny MeSH
Studying morphogenesis is unthinkable without visualizing shapes, and sharing the results of such studies critically depends on communicating image data. Despite a wealth of literature dealing with acquisition and analysis of image data, visualizing them for publication or presentation purposes remains a craft learned mainly by experience. This chapter provides a practical guide to producing publication-grade illustrations out of raw microscopic (or other) digital images, using mostly or exclusively free software, and points out some common problems and their solutions.
- Klíčová slova
- Bit depth, Bitmap, Computer graphics, Data visualization, ImageJ, Inkscape, Microscopy, Raster, Resolution, Vector,
- MeSH
- mikroskopie metody MeSH
- počítače MeSH
- počítačová grafika MeSH
- počítačové zpracování obrazu metody MeSH
- software * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
