Bioimage Dotaz Zobrazit nápovědu
Similar to the medical imaging community, the bioimaging community has recently realized the need to benchmark various image analysis methods to compare their performance and assess their suitability for specific applications. Challenges sponsored by prestigious conferences have proven to be an effective means of encouraging benchmarking and new algorithm development for a particular type of image data. Bioimage analysis challenges have recently complemented medical image analysis challenges, especially in the case of the International Symposium on Biomedical Imaging (ISBI). This review summarizes recent progress in this respect and describes the general process of designing a bioimage analysis benchmark or challenge, including the proper selection of datasets and evaluation metrics. It also presents examples of specific target applications and biological research tasks that have benefited from these challenges with respect to the performance of automatic image analysis methods that are crucial for the given task. Finally, available benchmarks and challenges in terms of common features, possible classification and implications drawn from the results are analysed.
- MeSH
- algoritmy MeSH
- benchmarking * MeSH
- databáze faktografické MeSH
- fluorescenční mikroskopie přístrojové vybavení metody normy MeSH
- lidé MeSH
- molekulární zobrazování přístrojové vybavení metody normy MeSH
- počítačové zpracování obrazu metody statistika a číselné údaje MeSH
- rozpoznávání automatizované statistika a číselné údaje MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
Image analysis is key to extracting quantitative information from scientific microscopy images, but the methods involved are now often so refined that they can no longer be unambiguously described by written protocols. We introduce BIAFLOWS, an open-source web tool enabling to reproducibly deploy and benchmark bioimage analysis workflows coming from any software ecosystem. A curated instance of BIAFLOWS populated with 34 image analysis workflows and 15 microscopy image datasets recapitulating common bioimage analysis problems is available online. The workflows can be launched and assessed remotely by comparing their performance visually and according to standard benchmark metrics. We illustrated these features by comparing seven nuclei segmentation workflows, including deep-learning methods. BIAFLOWS enables to benchmark and share bioimage analysis workflows, hence safeguarding research results and promoting high-quality standards in image analysis. The platform is thoroughly documented and ready to gather annotated microscopy datasets and workflows contributed by the bioimaging community.
- Klíčová slova
- benchmarking, bioimaging, community, deep learning, deployment, image analysis, reproducibility, software, web application,
- Publikační typ
- časopisecké články MeSH
The classification of bioimages plays an important role in several biological studies, such as subcellular localisation, phenotype identification and other types of histopathological examinations. The objective of the present study was to develop a computer-aided bioimage classification method for the classification of bioimages across nine diverse benchmark datasets. A novel algorithm was developed, which systematically fused the features extracted from nine different convolution neural network architectures. A systematic fusion of features boosts the performance of a classifier but at the cost of the high dimensionality of the fused feature set. Therefore, non-discriminatory and redundant features need to be removed from a high-dimensional fused feature set to improve the classification performance and reduce the time complexity. To achieve this aim, a method based on analysis of variance and evolutionary feature selection was developed to select an optimal set of discriminatory features from the fused feature set. The proposed method was evaluated on nine different benchmark datasets. The experimental results showed that the proposed method achieved superior performance, with a significant reduction in the dimensionality of the fused feature set for most bioimage datasets. The performance of the proposed feature selection method was better than that of some of the most recent and classical methods used for feature selection. Thus, the proposed method was desirable because of its superior performance and high compression ratio, which significantly reduced the computational complexity.
- Klíčová slova
- Bioimage classification, Convolutional neural networks, Evolutionary algorithms, Feature fusion, Pre-trained CNNs, Transfer learning,
- MeSH
- algoritmy * MeSH
- neuronové sítě (počítačové) * MeSH
- Publikační typ
- časopisecké články MeSH
(1) Background: The detection of DNA double-strand breaks in vitro using the phosphorylated histone biomarker (γH2AX) is an increasingly popular method of measuring in vitro genotoxicity, as it is sensitive, specific and suitable for high-throughput analysis. The γH2AX response is either detected by flow cytometry or microscopy, the latter being more accessible. However, authors sparsely publish details, data, and workflows from overall fluorescence intensity quantification, which hinders the reproducibility. (2) Methods: We used valinomycin as a model genotoxin, two cell lines (HeLa and CHO-K1) and a commercial kit for γH2AX immunofluorescence detection. Bioimage analysis was performed using the open-source software ImageJ. Mean fluorescent values were measured using segmented nuclei from the DAPI channel and the results were expressed as the area-scaled relative fold change in γH2AX fluorescence over the control. Cytotoxicity is expressed as the relative area of the nuclei. We present the workflows, data, and scripts on GitHub. (3) Results: The outputs obtained by an introduced method are in accordance with expected results, i.e., valinomycin was genotoxic and cytotoxic to both cell lines used after 24 h of incubation. (4) Conclusions: The overall fluorescence intensity of γH2AX obtained from bioimage analysis appears to be a promising alternative to flow cytometry. Workflow, data, and script sharing are crucial for further improvement of the bioimage analysis methods.
- Klíčová slova
- ImageJ, bioimage analysis, genotoxicity, high-throughput, in vitro testing,
- MeSH
- biologické markery analýza MeSH
- HeLa buňky MeSH
- lidé MeSH
- mikroskopie * MeSH
- pilotní projekty MeSH
- poškození DNA * MeSH
- reprodukovatelnost výsledků MeSH
- valinomycin toxicita MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- biologické markery MeSH
- valinomycin MeSH
The syntheses and biological applications of two novel fluorescent 9-phenylethynylpyronin analogues containing either carbon or silicon at the position 10 are reported. Both fluorescent probes exhibited a relatively strong fluorescence in methanol and phosphate buffer saline in the near-infrared region (705-738 nm) upon irradiation of either of their absorption maxima in the blue and red regions. The compounds showed high selectivity toward mitochondria in myeloma cells in vivo and allowed their visualization in a favored tissue-transparent window, which makes them promising NIR fluorescent tags for applications in bioimaging.
Multifunctional platforms will play a key role and gain more prominence in the field of personalized healthcare worldwide in the near future due to the ever-increasing number of patients suffering from cancer. Along with the development of efficient techniques for cancer treatment, a considerable effort should be devoted toward the exploration of an emerging class of materials with unique properties that might be beneficial in this context. Currently, 2D post-carbon materials, such as pnictogens (phosphorene, antimonene), transition metal dichalcogenides, and boron nitride, have become popular due to their efficient photothermal behavior, drug-loading capability, and low toxicity. This review underlines the recent progresses made in the abovementioned 2D materials for photothermal/photodynamic cancer therapies and their applicability in bioimaging applications.
- MeSH
- diagnostické zobrazování * MeSH
- fototerapie * MeSH
- indukovaná hypertermie * MeSH
- lidé MeSH
- nádory diagnostické zobrazování metabolismus terapie MeSH
- nanostruktury * chemie terapeutické užití MeSH
- nosiče léků * chemie terapeutické užití MeSH
- přechodné kovy * chemie terapeutické užití MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
- Názvy látek
- nosiče léků * MeSH
- přechodné kovy * MeSH
Raman imaging allows one to obtain spatially resolved chemical information in a nondestructive manner. Herein, we present analytical aspects of effective in situ and in vivo Raman imaging of algae and cyanobacteria from within their native rock habitats. Specifically, gypsum and halite inhabited by endolithic communities from the hyperarid Atacama Desert were analyzed. Raman imaging of these phototrophic colonization reveals a pigment composition within the aggregates that helps in understanding some of their adaptation strategies to survive in this harsh polyextreme environment. The study is focused on methodical aspects of Raman imaging acquisition and subsequent data processing. Point imaging is compared with line imaging in terms of their image quality, spatial resolution, spectral signal-to-noise ratio, time requirements, and risk of laser-induced sample alteration. The roles of excitation wavelength, exposure time, and step size of the imaging grid on successful Raman imaging results are also discussed. Graphical abstract.
- Klíčová slova
- Astrobiology, Bioimage, Geobiology, Image analysis, Raman mapping, Scytonemin,
- MeSH
- biologické pigmenty analýza MeSH
- ekosystém MeSH
- pouštní klima MeSH
- půdní mikrobiologie * MeSH
- Ramanova spektroskopie * metody MeSH
- sinice chemie MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- biologické pigmenty MeSH
Mitotic cell division in plants is a dynamic process playing a key role in plant morphogenesis, growth, and development. Since progress of mitosis is highly sensitive to external stresses, documentation of mitotic cell division in living plants requires fast and gentle live-cell imaging microscopy methods and suitable sample preparation procedures. This chapter describes, both theoretically and practically, currently used advanced microscopy methods for the live-cell visualization of the entire process of plant mitosis. These methods include microscopy modalities based on spinning disk, Airyscan confocal laser scanning, structured illumination, and light-sheet bioimaging of tissues or whole plant organs with diverse spatiotemporal resolution. Examples are provided from studies of mitotic cell division using microtubule molecular markers in the model plant Arabidopsis thaliana, and from deep imaging of mitotic microtubules in robust plant samples, such as legume crop species Medicago sativa.
- Klíčová slova
- Arabidopsis, Light-sheet microscopy, Medicago, Microtubules, Mitosis, Phragmoplast, Plant, Preprophase band, Spindle, Superresolution microscopy,
- MeSH
- Arabidopsis metabolismus fyziologie MeSH
- mikroskopie metody MeSH
- mikrotubuly fyziologie MeSH
- mitóza fyziologie MeSH
- proteiny asociované s mikrotubuly metabolismus MeSH
- proteiny huseníčku metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- proteiny asociované s mikrotubuly MeSH
- proteiny huseníčku MeSH
Carbon quantum dots as a novel type of carbon nanomaterials have attracted the attention of many researchers because of their unique optical, antibacterial, and anticancer properties as well as their biocompatibility. In this study, for the first time, carbon quantum dots were prepared from o-phenylenediamine dissolved in toluene by a solvothermal route. Subsequently, the prepared carbon quantum dots were encapsulated into polyurethane films by a swelling-encapsulation-shrink method. Analyses of the results obtained by different characterization methods (AFM, TEM, EDS, FTIR, photoluminescence, and EPR) indicate the significant influence of the precursor on structural, chemical, and optical properties. Antibacterial and cytotoxicity tests showed that these dots did not have any antibacterial potential, because of the low extent of reactive oxygen species production, and showed low dark cytotoxicity. By investigating the cellular uptake, it was established that these dots penetrated the HeLa cells and could be used as probes for bioimaging.
- Klíčová slova
- antibacterial, bioimaging, carbon quantum dots, precursor, reactive oxygen species,
- Publikační typ
- časopisecké články MeSH
"All-in-one" multifunctional nanomaterials, which can be visualized simultaneously by several imaging techniques, are required for the efficient diagnosis and treatment of many serious diseases. This report addresses the design and synthesis of upconversion magnetic NaGdF4:Yb3+/Er3+(Tm3+) nanoparticles by an oleic acid-stabilized high-temperature coprecipitation of lanthanide precursors in octadec-1-ene. The nanoparticles, which emit visible or UV light under near-infrared (NIR) irradiation, were modified by in-house synthesized PEG-neridronate to facilitate their dispersibility and colloidal stability in water and bioanalytically relevant phosphate buffered saline (PBS). The cytotoxicity of the nanoparticles was determined using HeLa cells and human fibroblasts (HF). Subsequently, the particles were modified by Bolton-Hunter-neridronate and radiolabeled by 125I to monitor their biodistribution in mice using single-photon emission computed tomography (SPECT). The upconversion and the paramagnetic properties of the NaGdF4:Yb3+/Er3+(Tm3+)@PEG nanoparticles were evaluated by photoluminescence, magnetic resonance (MR) relaxometry, and magnetic resonance imaging (MRI) with 1 T and 4.7 T preclinical scanners. MRI data were obtained on phantoms with different particle concentrations and during pilot long-time in vivo observations of a mouse model. The biological and physicochemical properties of the NaGdF4:Yb3+/Er3+(Tm3+)@PEG nanoparticles make them promising as a trimodal optical/MRI/SPECT bioimaging and theranostic nanoprobe for experimental medicine.
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
