Joanna Sekulska-Nalewajko

Neural network segmentation of images from stained cucurbits leaves with colour symptoms of biotic and abiotic stresses

Abstract The increased production of Reactive Oxygen Species (ROS) in plant leaf tissues is a hallmark of a plant’s reaction to various environmental stresses. This paper describes an automatic segmentation method for scanned images of cucurbits leaves stained to visualise ROS accumulation sites featured by specific colour hues and intensities. The leaves placed separately in the scanner view field on a colour background are extracted by thresholding in the RGB colour space, then cleaned from petioles to obtain a leaf blade mask. The second stage of the method consists in the classification of within mask pixels in a hue-saturation plane using two classes, determined by leaf regions with and without colour products of the ROS reaction. At this stage a two-layer, hybrid artificial neural network is applied with the first layer as a self-organising Kohonen type network and a linear perceptron output layer (counter propagation network type). The WTA-based, fast competitive learning of the first layer was improved to increase clustering reliability. Widrow–Hoff supervised training used at the output layer utilises manually labelled patterns prepared from training images. The generalisation ability of the network model has been verified by K-fold cross-validation. The method significantly accelerates the measurement of leaf regions containing the ROS reaction colour products and improves measurement accuracy.

Alleviation of nickel toxicity in wheat (Triticum aestivum L.) seedlings by selenium supplementation

Abstract Hydroponically grown wheat seedlings were treated with 50 μM N i and/or 15 μM Se. After a 7-day culture period, their growth parameters, N i, Se, F e, and M g contents, electrolyte leakage, photosynthetic pigment concentrations, and photochemical activity of photosystem II were determined. Exposure of wheat seedlings to N i alone resulted in reduction in the total shoot and root lengths, by 22% and 50%, respectively. Addition of Se to the N i-containing medium significantly improved the growth of these organs, compared to the seedlings subjected to N i alone. Application of Se decreased the accumulation of N i in shoots and roots and partially alleviated the N i-induced decrease in F e and M g concentations in shoots. Electrolyte leakage increased in response to N i stress, but in shoots it was diminished by Se supplementation. Exposure to N i led to a decrease in chlorophyll a and b contents and enhancement of chlorophyll a/b ratio, but did not influence the concentration of carotenoids. Enrichment of the N i-containing medium with Se significantly increased chlorophyll b content, compared to the seedlings treated with N i alone. Photochemical activity, estimated in terms of the maximum quantum yield of photosystem II , decreased in response to N i treatment but was significantly improved by simultaneous addition of Se. Results of our study suggest that alleviation of N i toxicity in wheat seedlings by Se supplementation may be related to limitation of N i uptake.

Automated image analysis for quantification of reactive oxygen species in plant leaves

The paper presents an image processing method for the quantitative assessment of ROS accumulation areas in leaves stained with DAB or NBT for H2O2 and O2- detection, respectively. Three types of images determined by the combination of staining method and background color are considered. The method is based on the principle of supervised machine learning with manually labeled image patterns used for training. The methods algorithm is developed as a JavaScript macro in the public domain Fiji (ImageJ) environment. It allows to select the stained regions of ROS-mediated histochemical reactions, subsequently fractionated according to the weak, medium and intense staining intensity and thus ROS accumulation. It also evaluates total leaf blade area. The precision of ROS accumulation area detection is validated by the Dice Similarity Coefficient in the case of manual patterns. The proposed framework reduces the computation complexity, once prepared, requires less image processing expertise than the competitive methods and represents a routine quantitative imaging assay for a general histochemical image classification.

An automatic segmentation method for scanned images of wheat root systems with dark discolourations

An automatic segmentation method for scanned images of wheat root systems with dark discolourations The analysis of plant root system images plays an important role in the diagnosis of plant health state, the detection of possible diseases and growth distortions. This paper describes an initial stage of automatic analysis—the segmentation method for scanned images of Ni-treated wheat roots from hydroponic culture. The main roots of a wheat fibrous system are placed separately in the scanner view area on a high chroma background (blue or red). The first stage of the method includes the transformation of a scanned RGB image into the HCI (Hue-Chroma-Intensity) colour space and then local thresholding of the chroma component to extract a binary root image. Possible chromatic discolourations, different from background colour, are added to the roots from blue or red chroma subcomponent images after thresholding. At the second stage, dark discolourations are extracted by local fuzzy c-means clustering of an HCI intensity image within the binary root mask. Fuzzy clustering is applied in local windows around the series of sample points on roots medial axes (skeleton). The performance of the proposed method is compared with hand-labelled segmentation for a series of several root systems.

Interaction between salt stress and angular leaf spot (Pseudomonas syringae pv lachrymans) in cucumber.

Summary We studied the effects of sequentially applied salt stress and Pseudomonas syringae pv lachrymans (Psl) infection in cucumber (Cucumis sativus L.). Infection development, shoot and root growth potential, the concentrations of chlorophyll and proline as well as electrolyte leakage, lipid peroxidation and H2O2 production were determined. Cucumber plants were first exposed to salt stress and irrigated for seven days with 50 or 100 mM NaCl and thereafter inoculated by Psl. Abiotic stress compromised the defence response to pathogen and disease severity was the highest in 100 mM NaCl-treated plants. The reduced performance of salinized plants under biotic stress could be related to salt stressinduced plant growth inhibition with leaf expansion being the most sensitive to salinity, decreased chlorophyll content, increased electrolyte leakage and prolonged H2O2 accumulation in leaves implying perturbations in redox homeostasis. The response of NaCl-treated and control plants to bacterial infection differed in terms of H2O2 generation and lipid peroxidation. This study confirmed that proline is an important component of local and systemic responses to salt stress and infection. The results contribute to our knowledge of the nature of plant response to a combination of abiotic and biotic stresses Streszczenie W pracy badano efekty sekwencyjnego działania stresu solnego i infekcji Pseudomonas syringae pv. lachrymans (Psl) u ogórka (Cucumis sativus). Analizowano rozwój infekcji, wzrost pędu i korzeni, stężenie chlorofilu i proliny oraz wyciek elektrolitów, peroksydację lipidów i generowanie H2O2. Rośliny ogórka poddawano stresowi solnemu, podlewając je przez siedem dni roztworem NaCl o stężeniu 50 mM lub 100 mM, a następnie zakażano zawiesiną bakterii Psl. Stres abiotyczny osłabiał odpowiedź obronną ogórka na infekcję. Największe nasilenie choroby stwierdzono u roślin traktowanych wcześniej 100 mM NaCl. Słabsze funkcjonowanie roślin zasolonych NaCl w warunkach stresu biotycznego mogło być spowodowane negatywnymi skutkami stresu solnego w postaci zahamowania wzrostu, a zwłaszcza rozwoju blaszki liściowej, obniżenia stężenia chlorofilu, zwiększenia wycieku elektrolitów i wydłużonego w czasie gromadzenia H2O2 w liściach, wskazującego na zaburzenia homeostazy redoks. Różnice w odpowiedzi roślin kontrolnych i traktowanych NaCl na infekcję bakteryjną dotyczyły generowania H2O2 i peroksydacji lipidów. Badania potwierdziły, że prolina jest ważnym elementem lokalnej i systemicznej odpowiedzi na stres solny i infekcję. Uzyskane wyniki poszerzają naszą wiedzę na temat odpowiedzi roślin na stres abiotyczny i biotyczny, działające w połączeniu

A New Idea of Fast Three-Dimensional Median Filtering for Despeckling of Optical Coherence Tomography Images

Abstract Median filtering has been widely used in image processing for noise removal because it can significantly reduce the power of noise while limiting edge blurring. This filtering is still a challenging task in the case of three-dimensional images containing up to a billion of voxels, especially for large size filtering windows. The authors encountered the problem when applying median filter to speckle noise reduction in optical coherence tomography images acquired by the Spark OCT systems. In the paper a new approach to the GPU (Graphics Processing Unit) based median smoothing has been proposed, which uses two-step evaluation of local intensity histograms stored in the shared memory of a graphic device. The solution is able to output about 50 million voxels per second while processing the neighbourhood of 125 voxels by Quadro K6000 graphic card configured on the Kepler architecture.

Digital image processing methods in biological structure recognition - a short review

This paper presents general methods of biological images processing. These techniques are oriented to better image interpretation. Many biological structures are difficult to recognize in the picture due to deficient light conditions, particle aggregations or erroneous similarity to other objects. We made the illustration of the function and result of few methods, adapted to image recognition and identification. The results of image preprocessing are presented based on real biological structure examples

The segmentation of meristematic Allium cell images and extraction of nuclei features for the purpose of mitotic index evaluation

This paper presents the segmentation method of Allium cell images preceding the extraction of nuclei features that are capable to distinguish interphase and mitotic events. The segmentation consists in the isolation of cell regions and then local edge-based thresholding of nuclei parts including the corrections of observed artefacts. The ability of the separation of mitotic phases groups was tested for the nuclei textural and shape features using information gain ratio and Bayesian classification error.

Three-dimensional model of flooding of the river floodplain - visualization of ecohydrological interactions

Ecohydrology is a scientific concept which suggests that the sustainable development of water resources has been dependent on the ability to maintain the ecosystem processes that have been established by evolution. These ecosystem processes regulate water and nutrient circulation and energy flow at the basin scale in two ways: biota are regulated by hydrology and hydrology is regulated by biota (Zalewski, 2000) (Zalewski, 2002). The simulation of hydrological processes allows us better managing of natural environment and industrial resources. Visualization of numerical results of these processes in 3D world is an original and new approach. Mathematical and graphical modules are separate each other, what makes the application practicable and in the future allowed use this model to another resolves

Automated image analysis for quantification of histochemical detection of reactive oxygen species and necrotic infection symptoms in plant leaves

In plants, the accelerated production of reactive oxygen species (ROS) is a common response to different stresses. We developed a computer method of leaf image analysis to automatically quantify the and H2O2 staining patterns in leaves. The quantification of histochemically detected ROS is given as a percentage of stained area partitioned according to the staining intensity and hence accumulation. Thus, this method expands the routine histochemical detection of ROS in situ. The same procedure can be also used to assess necrotic infection symptoms. In plants infected with necrotizing pathogens leaves can be simultaneously examined for pathogen-induced and H2O2 accumulation and infection development. This procedure allows rapid and accurate examination of many leaves and provides an advantage over the routine visual assessment of in situ histochemical detection of ROS and infection symptom development.