A photometric stereo-based 3D imaging system using computer vision and deep learning for tracking plant growth.

BACKGROUND: Tracking and predicting the growth performance of plants in different environments is critical for predicting the impact of global climate change. Automated approaches for image capture and analysis have allowed for substantial increases in the throughput of quantitative growth trait measurements compared with manual assessments. Recent work has focused on adopting computer vision and machine learning approaches to improve the accuracy of automated plant phenotyping. Here we present PS-Plant, a low-cost and portable 3D plant phenotyping platform based on an imaging technique novel to plant phenotyping called photometric stereo (PS). RESULTS: We calibrated PS-Plant to track the model plant Arabidopsis thaliana throughout the day-night (diel) cycle and investigated growth architecture under a variety of conditions to illustrate the dramatic effect of the environment on plant phenotype. We developed bespoke computer vision algorithms and assessed available deep neural network architectures to automate the segmentation of rosettes and individual leaves, and extract basic and more advanced traits from PS-derived data, including the tracking of 3D plant growth and diel leaf hyponastic movement. Furthermore, we have produced the first PS training data set, which includes 221 manually annotated Arabidopsis rosettes that were used for training and data analysis (1,768 images in total). A full protocol is provided, including all software components and an additional test data set. CONCLUSIONS: PS-Plant is a powerful new phenotyping tool for plant research that provides robust data at high temporal and spatial resolutions. The system is well-suited for small- and large-scale research and will help to accelerate bridging of the phenotype-to-genotype gap.

Broadly available imaging devices enable high-quality low-cost photometry.

This paper demonstrates that, for applications in resource-limited environments, expensive microplate spectrophotometers that are used in many central laboratories for parallel measurement of absorbance of samples can be replaced by photometers based on inexpensive and ubiquitous, consumer electronic devices (e.g., scanners and cell-phone cameras). Two devices, (i) a flatbed scanner operating in transmittance mode and (ii) a camera-based photometer (constructed from a cell phone camera, a planar light source, and a cardboard box), demonstrate the concept. These devices illuminate samples in microtiter plates from one side and use the RGB-based imaging sensors of the scanner/camera to measure the light transmitted to the other side. The broadband absorbance of samples (RGB-resolved absorbance) can be calculated using the RGB color values of only three pixels per microwell. Rigorous theoretical analysis establishes a well-defined relationship between the absorbance spectrum of a sample and its corresponding RGB-resolved absorbance. The linearity and precision of measurements performed with these low-cost photometers on different dyes, which absorb across the range of the visible spectrum, and chromogenic products of assays (e.g., enzymatic, ELISA) demonstrate that these low-cost photometers can be used reliably in a broad range of chemical and biochemical analyses. The ability to perform accurate measurements of absorbance on liquid samples, in parallel and at low cost, would enable testing, typically reserved for well-equipped clinics and laboratories, to be performed in circumstances where resources and expertise are limited.

Integration of novel low-cost colorimetric, laser photometric, and visual fluorescent techniques for rapid identification of falsified medicines in resource-poor areas: application to artemether-lumefantrine.

The availability of falsified antimalarial drugs can be reduced with effective drug regulatory agencies and proper enforcement. Fundamental to these agencies taking action, rapid identification must be made as soon as they appear in the market place. Since falsified antimalarials occur mostly in developing countries, performing drug analysis presents itself with unique challenges. A fundamental factor in choosing a useful technique is affordability and simplicity. Therefore, we suggest a three-tiered drug evaluation strategy for identifying a falsified drug in resource-poor areas. Tier I is a simple comparison of a tablet's weight and dimensions with official specifications. Tier II uses inexpensive photometric devices (laser and fluorescence) to evaluate a tablet. Suspicious samples from Tier I and II assessments are then subjected to a colorimetric assay for active ingredients identification and quantification. In this article, we evaluate a novel colorimetric assay for the simultaneous assessment of both lumefantrine and artemether in co-formulated Coartem™ tablets, and integrate the method with two novel, low-cost, fluorescence and laser photometric devices. Image analysis software is used for the assessments. Although artemether-lumefantrine is used as an example, the strategy may be adapted to other medicines.

Simultaneous and rapid determination of caffeine and taurine in energy drinks by MEKC in a short capillary with dual contactless conductivity/photometry detection.

A method has been developed for the simultaneous determination of taurine and caffeine using a laboratory-made instrument enabling separation analysis in a short 10.5 cm capillary. The substances are detected using a contactless conductometry/ultraviolet (UV) photometry detector that enables recording both signals at one place in the capillary. The separation of caffeine and taurine was performed using the MEKC technique in a BGE with the composition 40 mM CHES, 15 mM NaOH, and 50 mM SDS, pH 9.36. Under these conditions, the migration time of caffeine is 43 s and of taurine 60 s; LOD for caffeine is 4 mg/L using photometric detection and LOD for taurine is 24 mg/L using contactless conductometric detection. The standard addition method was used for determination in Red Bull energy drink of caffeine 317 mg/L and taurine 3860 mg/L; the contents in Kamikaze drink were 468 mg/L caffeine and 4110 mg/L taurine. The determined values are in good agreement with the declared contents of these substances. RSD does not exceed 3%.

A complete low cost radon detection system.

Monitoring the (222)Rn activity through the 1200 km long Northern Anatolian fault line, for the purpose of earthquake precursory, requires large number of cost effective radon detectors. We have designed, produced and successfully tested a low cost radon detection system (a radon monitor). In the detector circuit of this monitor, First Sensor PS100-7-CER-2 windowless PIN photodiode and a custom made transempedence/shaping amplifier were used. In order to collect the naturally ionized radon progeny to the surface of the PIN photodiode, a potential of 3500 V was applied between the conductive hemi-spherical shell and the PIN photodiode. In addition to the count rate of the radon progeny, absolute pressure, humidity and temperature were logged during the measurements. A GSM modem was integrated to the system for transferring the measurements from the remote locations to the data process center.

A cost-effective solution for the reliable determination of cell numbers of microorganisms in liquid culture.

The concentration of microorganisms in growth medium is an important parameter in microbiological research. One of the approaches to determine this parameter is based on the physical interaction of small particles with light that results in light scattering. Table-top spectrophotometers can be used to determine the scattering properties of a sample as a change in light transmission. However, a portable, reliable, and maintenance-free instrument that can be built from inexpensive parts could provide new research opportunities. In this report, we show how to build such an instrument. This instrument consists of a low power monochromatic light-emitting diode, a monolithic photodiode, and a microcontroller. We demonstrate that this instrument facilitates the precise determination of cell concentrations for the bacteria Escherichia coli and Pseudomonas aeruginosa as well as the cyanobacterium Synechocystis sp. PCC 6803 and the green alga Chlamydomonas reinhardtii.

Hemoglobin determination with paired emitter detector diode.

Two ordinary green light-emitting diodes used as light emitter and detector coupled with simple voltmeter form a complete, cost-effective prototype of a photometric hemoglobinometer. The device has been optimized for cuvette assays of total hemoglobin (Hb) in diluted blood using three different chemical methods recommended for the needs of clinical analysis (namely Drabkin, lauryl sulfate, and dithionite methods). The utility of developed device for real analytics has been validated by the assays of total Hb content in human blood. The results of analysis are fully compatible with those obtained using clinically recommended method and clinical analyzer.

An inexpensive, portable and microcontrolled near infrared LED-photometer for screening analysis of gasoline.

A microcontrolled, portable and inexpensive photometer is proposed. It uses a near infrared light emitting diode (NIR LED) as radiation source, a PbSe photoresistor as infrared detector and a programmable interrupt controller (PIC) microcontroller as control unit. The detector system presents a thermoresistor and a thermoelectric cooling to control the detector temperature and keep the noise at low levels. The microcontroller incorporated total autonomy on the proposed photometer. As its components are inexpensive and of easy acquisition, the proposed NIR LED-photometer is an economical alternative for chemical analyses in small routine, research and/or teaching laboratories. By being portable and microcontrolled, it also allows carrying out field chemical analyses. The instrument was successfully applied on the screening analysis to verify adulteration in gasoline samples.

Low-cost, multimodal, portable screening system for early detection of oral cancer.

Oral cancer is an important global health problem. There is an urgent need for improved methods to detect oral cancer and its precursors, because early detection is the best way to reduce oral cancer mortality and morbidity. In this work, we describe simple modifications to a surgical headlight system that enables direct visualization and digital image acquisition from oral tissue in multiple imaging modalities including fluorescence, white-light reflectance, and orthogonal polarization reflectance. Images obtained with the system in-vivo demonstrate that it is an attractive technology to explore for oral cancer screening in low-resource environments where clinical expertise is often unavailable.

Cost-effective diffuse reflectance spectroscopy device for quantifying tissue absorption and scattering in vivo.

A hybrid optical device that uses a multimode fiber coupled to a tunable light source for illumination and a 2.4-mm photodiode for detection in contact with the tissue surface is developed as a first step toward our goal of developing a cost-effective, miniature spectral imaging device to map tissue optical properties in vivo. This device coupled with an inverse Monte Carlo model of reflectance is demonstrated to accurately quantify tissue absorption and scattering in tissue-like turbid synthetic phantoms with a wide range of optical properties. The overall errors for quantifying the absorption and scattering coefficients are 6.0+/-5.6 and 6.1+/-4.7%, respectively. Compared with fiber-based detection, having the detector right at the tissue surface can significantly improve light collection efficiency, thus reducing the requirement for sophisticated detectors with high sensitivity, and this design can be easily expanded into a quantitative spectral imaging system for mapping tissue optical properties in vivo.

Application of low-cost Gallium Arsenide light-emitting-diodes as kerma dosemeter and fluence monitor for high-energy neutrons.

Displacement damage (DD) caused by fast neutrons in unbiased Gallium Arsenide (GaAs) light emitting diodes (LED) resulted in a reduction of the light output. On the other hand, a similar type of LED irradiated with gamma rays from a (60)Co source up to a dose level in excess of 1.0 kGy (1.0 x 10(5) rad) was found to show no significant drop of the light emission. This phenomenon was used to develop a low cost passive fluence monitor and kinetic energy released per unit mass dosemeter for accelerator-produced neutrons. These LED-dosemeters were used to assess the integrated fluence of photoneutrons, which were contaminated with a strong bremsstrahlung gamma-background generated by the 730 MeV superconducting electron linac driving the free electron laser in Hamburg (FLASH) at Deutsches Elektronen-Synchrotron. The applications of GaAs LED as a routine neutron fluence monitor and DD precursor for the electronic components located in high-energy accelerator environment are highlighted.

A cost-effective line-based light-balancing technique using adaptive processing.

The camera imaging system has been widely used; however, the displaying image appears to have an unequal light distribution. This paper presents novel light-balancing techniques to compensate uneven illumination based on adaptive signal processing. For text image processing, first, we estimate the background level and then process each pixel with nonuniform gain. This algorithm can balance the light distribution while keeping a high contrast in the image. For graph image processing, the adaptive section control using piecewise nonlinear gain is proposed to equalize the histogram. Simulations show that the performance of light balance is better than the other methods. Moreover, we employ line-based processing to efficiently reduce the memory requirement and the computational cost to make it applicable in real-time systems.

A simple low-cost microcontroller-based photometric instrument for monitoring chloroplast movement.

A new microcontroller-based photometric instrument for monitoring blue light dependent changes in leaf transmission (chloroplast movement) was developed based on a modification of the double-beam technique developed by Walzcak and Gabrys [(1980) Photosynthetica 14: 65-72]. A blue and red bicolor light emitting diode (LED) provided both a variable intensity blue actinic light and a low intensity red measuring beam. A phototransistor detected the intensity of the transmitted measuring light. An inexpensive microcontroller independently and precisely controlled the light emission of the bicolor LED. A typical measurement event involved turning off the blue actinic light for 100 mus to create a narrow temporal window for turning on and measuring the transmittance of the red light. The microcontroller was programmed using LogoChip Logo (http://www.wellesley.edu/Physics/Rberg/logochip/) to record fluence rate response curves. Laser scanning confocal microscopy was utilized to correlate the changes in leaf transmission with intercellular chloroplast position. In the dark, the chloroplasts in the spongy mesophyll exhibited no evident asymmetries in their distribution, however, in the palisade layer the cell surface in contact with the overlying epidermis was devoid of chloroplasts. The low light dependent decrease in leaf transmittance in dark acclimated leaves was correlated with the movement of chloroplasts within the palisade layer into the regions previously devoid of chloroplasts. Changes in leaf transmittance were evident within one minute following the onset of illumination. Minimal leaf transmittance was correlated with chloroplasts having retreated from cell surfaces perpendicular to the incident light (avoidance reaction) in both spongy and palisade layers.

Low-cost system for real-time monitoring of luciferase gene expression.

In some mammalian cells transfected with luciferase reporter genes, the luciferase/luciferin reaction in a cell monolayer produces a very small light flux. While the low light levels are often measurable with single-photon counting cameras, these devices are expensive and may require long averaging times to acquire an image. We describe an approach for real-time monitoring of light produced by luciferase gene expression in intact, cultured cells using readily available and relatively inexpensive components. The system uses a single-photon counting photomultiplier tube with built-in high voltage supply and photon counting circuitry to rapidly measure average light output from growing cells in a 35 mm culture dish. The fast, accurate and highly sensitive response of the system makes it useful for studying the dynamics of gene expression over time periods ranging from minutes to days.

Improved strategy for screening prospective blood donors for anaemia.

Women (568) and men (531) attending blood donation sessions in Wessex in September, 1992, were assessed for anaemia by the standard CuSO4 method on finger-prick (FP) blood samples. The haemoglobin (Hb) concentration on FP samples and on venous blood was also checked using the HemoCue. Different FP samples from the same donors revealed a wide variation on HemoCue. We recommend retaining the CuSO4 method on FP samples as the initial screen, and follow-up of apparent failures by determining the Hb concentration on venous sampling with the HemoCue. As 54% of females were found on venous samples to be below the current recommended threshold (125 g/L) for Hb concentration, we also recommend lowering the threshold to 115 g/L for women, and to 130 g/L for men. We further recommend a close re-examination of normal haematology values for adults.

Dry chemistry instruments in primary care. I. Operating conditions and financial considerations.

The objectives of this study were to describe the operating conditions of dry chemistry instruments in primary care, as well as to elucidate financial aspects in general practice fee-for-service settings. We used questionnaires mailed to all users of the two most used dry chemistry instruments in Norway, as well as to a 14% random sample of Norwegian GPs. The overall response rate was 79%. The mean number of dry chemistry analyses varied considerably between individual users, but in general a substantial number of analyses were carried out. Even though most analyses on the instruments' repertoire were available in all user groups, a total of 13 additional constituents were suggested to be included in the repertoire. In occupational health care most results were ready when the client was present; this was not the case in general practice. The instruments were more profitable when more constituents were analysed per sample, although profitability varied substantially in the period studied (1986-1989). A discrete time history event analysis revealed that net profit earned, lower instrument price, available information about the technology and being in solo practice significantly influenced the decision to buy an instrument in fee-for-service practices.