Image segmentation is a key process in analyzing biological images. However, it is difficult to detect the differences between foreground and background when the image is unevenly illuminated. The unambiguous segmenting of multi-well plate microscopy images with various uneven illuminations is a challenging problem. Currently, no publicly available method adequately solves these various problems in bright-field multi-well plate images. Here, we propose a new method based on contrast values which removes the need for illumination correction. The presented method is effective enough to distinguish foreground and therefore a model organism (Caenorhabditis elegans) from an unevenly illuminated microscope image. In addition, the method also can solve a variety of problems caused by different uneven illumination scenarios. By applying this methodology across a wide range of multi-well plate microscopy images, we show that our approach can consistently analyze images with uneven illuminations with unparalleled accuracy and successfully solve various problems associated with uneven illumination. It can be used to process the microscopy images captured from multi-well plates and detect experimental subjects from an unevenly illuminated background.

We present a simple, fast method for thickness characterization of suspended graphene/graphite flakes that is based on transmission electron microscopy (TEM). We derive an analytical expression for the intensity of the transmitted electron beam I0(t), as a function of the specimen thickness t (t<<λ; where λ is the absorption constant for graphite). We show that in thin graphite crystals the transmitted intensity is a linear function of t. Furthermore, high-resolution (HR) TEM simulations are performed to obtain λ for a 001 zone axis orientation, in a two-beam case and in a low symmetry orientation. Subsequently, HR (used to determine t) and bright-field (to measure I0(0) and I0(t)) images were acquired to experimentally determine λ. The experimental value measured in low symmetry orientation matches the calculated value (i.e., λ=225±9 nm). The simulations also show that the linear approximation is valid up to a sample thickness of 3–4 nm regardless of the orientation and up to several ten nanometers for a low symmetry orientation. When compared with standard techniques for thickness determination of graphene/graphite, the method we propose has the advantage of being simple and fast, requiring only the acquisition of bright-field images.

Distribution of wax in laser printer toner was observed using an ultra-high-voltage (UHV) and a medium-voltage transmission electron microscope (TEM). As the radius of the wax spans a hundred to greater than a thousand nanometers, its three-dimensional recognition via TEM requires large depth of focus (DOF) for a volumetric specimen. A tomogram with a series of the captured images would allow the determination of their spatial distribution. In this study, bright-field (BF) images acquired with UHV-TEM at a high tilt angle prevented the construction of the tomogram. Conversely, the Z-contrast images acquired by the medium-voltage TEM produced a successful tomogram. The spatial resolution for both is discussed, illustrating that the image degradation was primarily caused by beam divergence of the Z-contrast image and the combination of DOF and chromatic aberration of the BF image from the UHV-TEM.

In variable phase bright-field contrast, a bright-field image based on axial or concentric-peripheral light is optically superimposed with a phase-contrast image, so that typical details that are imminent in one or the other technique contribute to the resulting composite image. In particular, complex structured specimens consisting of high-density light absorbing details and additional low-density phase shifting components can be observed with improved clarity. As both partial images interfere with each other, fine details within thin specimens can be highlighted further by additional contrast effects based on interference. Haloing and shade-off are significantly reduced when compared with phase contrast carried out stand-alone. Our method is characterized by several technical means that are relevant for the high image quality that can be achieved: both illuminating light components associated with bright field and phase contrast are filtered at different colors and separated from each other so that they meet the specimen at different angles of incidence. The intensities of the phase-contrast- and bright-field-producing light can be selectively regulated so that the final image can be dominated by phase contrast or bright field, or be equalized. The condenser aperture diaphragm can be used for modulations of the image's appearance.

Monochrome astronomy filters are well suited for use as excitation or suppression filters in fluorescence microscopy. Because of their particular optical design, such filters can be combined with standard halogen light sources for excitation in many fluorescent probes. In this “low energy excitation,” photobleaching (fading) or other irritations of native specimens are avoided. Photomicrographs can be taken from living motile fluorescent specimens also with a flash so that fluorescence images can be created free from indistinctness caused by movement. Special filter cubes or dichroic mirrors are not needed for our method. By use of suitable astronomy filters, fluorescence microscopy can be carried out with standard laboratory microscopes equipped with condensers for bright-field (BF) and dark-field (DF) illumination in transmitted light. In BF excitation, the background brightness can be modulated in tiny steps up to dark or black. Moreover, standard industry microscopes fitted with a vertical illuminator for examinations of opaque probes in DF or BF illumination based on incident light (wafer inspections, for instance) can also be used for excitation in epi-illumination when adequate astronomy filters are inserted as excitatory and suppression filters in the illuminating and imaging light path. In all variants, transmission bands can be modulated by transmission shift.

Different approaches using microscopy image analysis procedures were employed for characterization of activated sludge systems. The approaches varied mainly on the type of visualization and acquisition method used for collection of data. In this context, this study focused on the comparison of the two most common acquisition methods: bright field and phase-contrast microscopy. Images were acquired from seven different wastewater treatment plants for a combined period of two years. Advantages and disadvantages of each acquisition technique and the results are discussed. Bright field microscopy proved to be more simple and inexpensive and provided the best overall results.