Current methods of in-house plant phenotyping are providing a powerful new tool for plant biology studies. The self-constructed and commercial platforms established in the last few years, employ non-destructive methods and measurements on a large and high-throughput scale. The platforms offer to certain extent, automated measurements, using either simple single sensor analysis, or advanced integrative simultaneous analysis by multiple sensors. However, due to the complexity of the approaches used, it is not always clear what such forms of plant phenotyping can offer the potential end-user, i.e. plant biologist. This review focuses on imaging methods used in the phenotyping of plant shoots including a brief survey of the sensors used. To open up this topic to a broader audience, we provide here a simple introduction to the principles of automated non-destructive analysis, namely RGB, chlorophyll fluorescence, thermal and hyperspectral imaging. We further on present an overview on how and to which extent, the automated integrative in-house phenotyping platforms have been used recently to study the responses of plants to various changing environments.

• Klíčová slova
• Biomass production, Chlorophyll fluorescence imaging, Hyperspectral imaging, Plant phenotyping, RGB digital imaging, Shoot growth, Thermal imaging,
• Publikační typ
• časopisecké články MeSH

BACKGROUND: Recently emerging approaches to high-throughput plant phenotyping have discovered their importance as tools in unravelling the complex questions of plant growth, development and response to the environment, both in basic and applied science. High-throughput methods have been also used to study plant responses to various types of biotic and abiotic stresses (drought, heat, salinity, nutrient-starving, UV light) but only rarely to cold tolerance. RESULTS: We present here an experimental procedure of integrative high-throughput in-house phenotyping of plant shoots employing automated simultaneous analyses of shoot biomass and photosystem II efficiency to study the cold tolerance of pea (Pisum sativum L.). For this purpose, we developed new software for automatic RGB image analysis, evaluated various parameters of chlorophyll fluorescence obtained from kinetic chlorophyll fluorescence imaging, and performed an experiment in which the growth and photosynthetic activity of two different pea cultivars were followed during cold acclimation. The data obtained from the automated RGB imaging were validated through correlation of pixel based shoot area with measurement of the shoot fresh weight. Further, data obtained from automated chlorophyll fluorescence imaging analysis were compared with chlorophyll fluorescence parameters measured by a non-imaging chlorophyll fluorometer. In both cases, high correlation was obtained, confirming the reliability of the procedure described. CONCLUSIONS: This study of the response of two pea cultivars to cold stress confirmed that our procedure may have important application, not only for selection of cold-sensitive/tolerant varieties of pea, but also for studies of plant cold-response strategies in general. The approach, provides a very broad tool for the morphological and physiological selection of parameters which correspond to shoot growth and the efficiency of photosystem II, and is thus applicable in studies of various plant species and crops.

• Klíčová slova
• Biomass production, Chlorophyll fluorescence imaging, Cold adaptation, Pea (Pisum), Plant phenotyping, RGB digital imaging, Shoot growth,
• Publikační typ
• časopisecké články MeSH

The human age for medico-legal purposes is usually estimated from hard tissues like bones and teeth. Only little attention was paid to soft tissues most probably due to the lack of detectable age changes. This study deals with colour changes of human tissue from intervertebral discs, Achilles tendon and rib cartilage in the relation to the age. The image analysis of colour of investigated tissue samples was performed. The values of intensities of channels RGB (MeanRed, MeanGreen, and MeanBlue) and parameters from the IHS system (MeanSaturation, HueTypical, HueVariation, BrightVariation and MeanBrightness) were evaluated. The results confirm that colour changes of some tissues can be used for age estimation.

• MeSH
• Achillova šlacha patologie   MeSH
• chrupavka patologie   MeSH
• meziobratlová ploténka patologie   MeSH
• počítačové zpracování obrazu * MeSH
• soudní lékařství metody   MeSH
• spektrofotometrie * MeSH
• stárnutí patologie   MeSH
• sulfasalazin MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• sulfasalazin MeSH

Automated analysis of small and optically variable plant organs, such as grain spikes, is highly demanded in quantitative plant science and breeding. Previous works primarily focused on the detection of prominently visible spikes emerging on the top of the grain plants growing in field conditions. However, accurate and automated analysis of all fully and partially visible spikes in greenhouse images renders a more challenging task, which was rarely addressed in the past. A particular difficulty for image analysis is represented by leaf-covered, occluded but also matured spikes of bushy crop cultivars that can hardly be differentiated from the remaining plant biomass. To address the challenge of automated analysis of arbitrary spike phenotypes in different grain crops and optical setups, here, we performed a comparative investigation of six neural network methods for pattern detection and segmentation in RGB images, including five deep and one shallow neural network. Our experimental results demonstrate that advanced deep learning methods show superior performance, achieving over 90% accuracy by detection and segmentation of spikes in wheat, barley and rye images. However, spike detection in new crop phenotypes can be performed more accurately than segmentation. Furthermore, the detection and segmentation of matured, partially visible and occluded spikes, for which phenotypes substantially deviate from the training set of regular spikes, still represent a challenge to neural network models trained on a limited set of a few hundreds of manually labeled ground truth images. Limitations and further potential improvements of the presented algorithmic frameworks for spike image analysis are discussed. Besides theoretical and experimental investigations, we provide a GUI-based tool (SpikeApp), which shows the application of pre-trained neural networks to fully automate spike detection, segmentation and phenotyping in images of greenhouse-grown plants.

• Klíčová slova
• automated plant phenotyping, deep learning, high-throughput plant image analysis, spike detection, spike segmentation,
• MeSH
• jedlá semena MeSH
• listy rostlin MeSH
• neuronové sítě * MeSH
• počítačové zpracování obrazu MeSH
• šlechtění rostlin * MeSH
• Publikační typ
• časopisecké články MeSH

Video rate confocal laser scanning microscopy at the highest spatial and temporal resolution of backscattered light (BSL) imaging allowed for regular observation of fast intracellular motion (FIM) first revealed in living neoplastic cells. However, the absence of an objective evaluation has hampered further study of the mechanisms and biological significance of FIM. Particularly, a quantification of apparent differences in velocities that would complement and improve the current demonstration of FIM by color coding using the combination of red-green-blue (RGB) images had been missing. Standard methods of tracking or pattern recognition could not be applied because of the fuzzy nature of images of FIM. A search for a suitable method led to correlation analysis. It was calibrated on Brownian motion and a known type of motion, such as cell marginal ruffling, compared with FIM. Results approved its explanatory potential. Therefore, several crucial incidences of FIM could be analyzed. Apart from an argument against viewing FIM as a manifestation of simple Brownian motion, the correlation analysis of FIM in the adjacent peripheries of a rat fibroblast and a K4 rat sarcoma cell confirmed the notion of higher and uneven distribution of velocity of FIM in a tumor cell so far shown in color-coded images only. This result and other yet unpublished observations indicate that the velocity and topology of FIM can also contribute to a biological distinction between neoplastic and normal cells. Regular application of the correlation analysis should further expand the study of FIM for its mechanisms and predictive value. Such an approach should be thoroughly examined for a contribution to the knowledge of cancer cells.

• MeSH
• audiovizuální záznam MeSH
• experimentální sarkom MeSH
• fibroblasty cytologie   fyziologie   MeSH
• kalibrace MeSH
• konfokální mikroskopie metody   MeSH
• krysa rodu Rattus MeSH
• kultivované buňky fyziologie   MeSH
• listy rostlin cytologie   fyziologie   MeSH
• nádorové buňky kultivované fyziologie   MeSH
• počítačové zpracování obrazu MeSH
• pohyb buněk fyziologie   MeSH
• zobrazování trojrozměrné MeSH
• zvířata MeSH
• Check Tag
• krysa rodu Rattus MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

This study deals with age estimation based on colour changes of human tissue from the intervertebral discs, Achilles tendon and rib cartilage. The investigated colour changes are the result of the accumulation of non-enzymatic browning products in the tissue. Samples of excised tissues were photographed with a digital camera and the pictures were evaluated using the image analysis processor Lucia G 4.11 processor. The values of the intensities of the RGB channels (MeanRed, Mean Green, MeanBlue) and parameters from the IHS system (MeanSaturation, HueTypical, HueVariation, BrightVariation and MeanBrightness) were evaluated. The results confirm that colour changes of some tissues depend on ageing and are a good tool for age estimation.

• MeSH
• Achillova šlacha patologie   MeSH
• barva * MeSH
• biologické markery MeSH
• chrupavka patologie   MeSH
• dospělí MeSH
• fotografování MeSH
• lidé středního věku MeSH
• lidé MeSH
• meziobratlová ploténka patologie   MeSH
• mladiství MeSH
• počítačové zpracování obrazu MeSH
• produkty pokročilé glykace metabolismus   MeSH
• reprodukovatelnost výsledků MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• soudní vědy přístrojové vybavení   metody   MeSH
• stárnutí patologie   MeSH
• žebra MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladiství MeSH
• mužské pohlaví MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• biologické markery MeSH
• produkty pokročilé glykace MeSH

Smartphones are widely spread and their usage does not require any trained personnel. Recently, smartphones were successfully used in analytical chemistry as a simple detection tool in some applications. This paper focuses on immobilization of acetylcholinesterase (AChE) onto commercially available pH strips with stabilization in the gelatin membrane. AChE degrades acetylcholine into choline and acetic acid which causes color change of acid-base indicator. Smartphone served as a tool for measurement of indicator color change from red to orange while inhibitors blocked this process. AChE inhibitors were measured with limits of detection, 149 nM and 22.3 nM for galanthamine and donepezil, respectively. Organic solvents were measured for method interferences. Measurement procedure was performed on 3D printed holder and digital photography was evaluated using red-green-blue (RGB) channels. The invented assay was validated to the standard Ellman's test and verified on murine plasma samples spiked with inhibitors. We consider that the assay is fully suitable for practical performance.

• Publikační typ
• časopisecké články MeSH

In radiotherapy, radiochromic films can be used for verification of delivery of dose distributions calculated by treatment planning systems. The main objective of this work was to compare three different techniques for evaluation of dose distributions for prostate cancer treatment plans using radiochromic EBT3 films. These techniques are: red channel evaluation taking into account only a response of irradiated film (R), red channel evaluation taking into account a response of unirradiated and irradiated film (Rcor) and multichannel evaluation in FilmQA software (RGB). Also comparison between film and MatriXX measurement was performed. Comparison showed that gamma analysis passing rates strongly depend on evaluation technique and on a model of scanner for digitizing films. The highest gamma passing rates were obtained with red channel evaluation taking into account a response of unirradiated and irradiated film using Epson V750 scanner (Rcor) and multichannel evaluation in FilmQA using Epson 11000XL scanner.

• MeSH
• algoritmy MeSH
• celková dávka radioterapie MeSH
• fantomy radiodiagnostické * MeSH
• filmová dozimetrie přístrojové vybavení   metody   MeSH
• kalibrace MeSH
• lidé MeSH
• nádory prostaty radioterapie   MeSH
• plánování radioterapie pomocí počítače metody   MeSH
• radioterapie s modulovanou intenzitou metody   MeSH
• záření gama MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• hodnotící studie MeSH
• srovnávací studie MeSH

Colorimetry is a widely used technique for optical detection in point-of-care testing and on-site detection. Although some studies employ a multiplex approach to analyse coloured solutions, many still analyse one sample at a time. We have prepared a simple and affordable colorimetric assay based on a TCS34725 colour sensor (ams-OSRAM) integrated into an M5Stack module and an RGB LED module both inserted into a 3D printed frame. We found that the colorimetric assay can be easily transferred to a colour sensing platform, and the signal range obtained using the prepared colorimeter is more than 200 times larger than that obtained using digital image colorimetry (DIC) for the same samples containing cholinesterase or urease as a model enzyme providing a change in pH of the processed solution. The assay appears to be ready for practical use.

• MeSH
• kolorimetrie * přístrojové vybavení   metody   MeSH
• koncentrace vodíkových iontů MeSH
• ureasa chemie   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• ureasa MeSH