Robust detection and localization of biomolecules inside cells is of great importance to better understand the functions related to them. Fluorescence microscopy and specific staining methods make biomolecules appear as point-like signals on image data, often acquired in 3D. Visual detection of such point-like signals can be time consuming and problematic if the 3D images are large, containing many, sometimes overlapping, signals. This sets a demand for robust automated methods for accurate detection of signals in 3D fluorescence microscopy. We propose a new 3D point-source signal detection method that is based on Fourier series. The method consists of two parts, a detector, which is a cosine filter to enhance the point-like signals, and a verifier, which is a sine filter to validate the result from the detector. Compared to conventional methods, our method shows better robustness to noise and good ability to resolve signals that are spatially close. Tests on image data show that the method has equivalent accuracy in signal detection in comparison to Visual detection by experts. The proposed method can be used as an efficient point-like signal detection tool for various types of biological 3D image data.
Cell cultures as well as cells in tissue always display a certain degree of variability,and measurements based on cell averages will miss important information contained in a heterogeneous population. These differences among cells in a population may be essential to quantify when looking at, e.g., protein expression and mutations in tumor cells which often show high degree of heterogeneity.
Single nucleotide mutations in the mithochondrial DNA (mtDNA) can accumulate and later be present in large proportions of the mithocondria causing devastating diseases. To study mtDNA accumulation and segregation one needs to measure the amount of mtDNA mutations in each cell in multiple serial cell culture passages. The different degrees of mutation in a cell culture can be quantified by making measurements on individual cells as an alternative to looking at an average of a population. Fluorescence microscopy in combination with automated digital image analysis provides an efficient approach to this type of single cell analysis.
Image analysis software for these types of applications are often complicated and not easy to use for persons lacking extensive knowledge in image analysis, e.g., laboratory personnel. This paper presents a user friendly implementation of an automated method for image based measurements of mtDNA mutations in individual cells detected with padlock probes and rolling-circle amplification (RCA). The mitochondria are present in the cell’s cytoplasm, and here each cytoplasm has to be delineated without the presence of a cytoplasmic stain. Three different methods for segmentation of cytoplasms are compared and it is shown that automated cytoplasmic delineation can be performed 30 times faster than manual delineation, with an accuracy as high as 87%. The final image based measurements of mitochondrial mutation load are also compared to, and show high agreement with, measurements made using biochemical techniques.
Cell cultures as well as cells in tissue always display a certain degree of variability, and measurements based on cell averages will miss important information contained in a heterogeneous population. This paper presents automated methods for image based measurements of mitochondiral DNA (mtDNA) mutations in individual cells. The mitochondria are present in the cell’s cytoplasm, and each cytoplasm has to be delineated. Three different methods for segmentation of cytoplasms are compared and it is shown that automated cytoplasmic delineation can be performed 30 times faster than manual delineation, with an accuracy as high as 87%. The final image based measurements of mitochondrial mutation load are also compared to, and show high agreement with, measurements made using biochemical techniques.
Images can be acquired at high rates with modern fluorescence microscopy hardware, giving rise to a demand for high-speed analysis of image data. Digital image cytometry, i.e., automated measurements and extraction of quantitative data from images of cells, provides valuable information for many types of biomedical analysis. There exists a number of different image analysis software packages that can be programmed to perform a wide array of useful measurements. However, the multi-application capability often compromises the simplicity of the tool. Also, the gain in speed of analysis is often compromised by time spent learning complicated software. We provide a free software called BlobFinder that is intended for a limited type of application, making it easy to use, easy to learn and optimized for its particular task. BlobFinder can perform batch processing of image data and quantify as well as localize cells and point like source signals in fluorescence microscopy images, e.g., from FISH, in situ PLA and padlock probing, in a fast and easy way.
Detection and localization of point-source signals is an important task in many image analysis applications. These types of signals can commonly be seen in fluorescent microscopy when studying functions of biomolecules. Visual detection and localization of point-source signals in 3D is limited and time consuming, making automated methods an important task. The 3D Stable Wave Detector (3DSWD) is a new method that combines signal enhancement with a verifier/separator. The verifier/separator examines the intensity gradient around a signal, making the detection less sensitive to noise and better at separating spatially close signals. Conventional methods such as; TopHat, Difference of Gaussian, and Multiscale Product consist only of signal enhancement. In this paper we compare the 3DSWD to these conventional methods with and without the addition of a verifier/separator. We can see that the 3DSWD has the highest robustness to noise among all the methods and that the other methods are improved when a verifier/separator is added.
Cell cultures as well as cells in tissue always display a certain degree of variability, and measurements based on cell averages will miss important information contained in a heterogeneous population. This paper presents automated methods for segmentation of cells and cytoplasms. The segmentation results are applied to image based measurements of mitochondiral DNA (mtDNA) mutations in individual cells. Three different methods for segmentation of cytoplasms are compared and it is shown that automated cytoplasmic delineation can be performed 30 times faster than manual delineation, with an accuracy as high as 87%, compared to an inter observer variability of 79% at manual delineation.
Paper-reinforced plastics are gaining increased interest as packaging materials, where mechanical properties are of great importance. Strength and stress transfer in paper sheets are controlled by fibre–fibre bonds. In paper-reinforced plastics, where the sheet is impregnated with a polymer resin, other stress-transfer mechanisms may be more important. The influence of fibre–fibre bonds on the strength of paper-reinforced plastics was therefore investigated. Paper sheets with different degrees of fibre–fibre bonding were manufactured and used as reinforcement in a polymeric matrix. Image analysis tools were used to verify that the difference in the degree of fibre–fibre bonding had been preserved in the composite materials. Strength and stiffness of the composites were experimentally determined and showed no correlation to the degree of fibre–fibre bonding, in contrast to the behaviour of unimpregnated paper sheets. The degree of fibre–fibre bonding is therefore believed to have little importance in this type of material, where stress is mainly transferred through the fibre–matrix interface.
Recent dramatic bleaching events on coral reefs have enhanced the need for global environmental monitoring. This paper investigates the value of present high spatial resolution satellites to detect coral bleaching using a change detection technique. We compared an IRS LISS-III image taken during the 1998 bleaching event in Belize to images taken before the bleaching event. The sensitivity of the sensors was investigated and a simulation was made to estimate the effect of sub-pixel changes. A manual interpretation of coral bleaching, based on differences between the images, was performed and the outcome were compared to field observations. The spectral characteristics of the pixels corresponding to the field observations and the manually interpreted bleachings have been analysed and compared to pixels from unaffected areas.
We devised a method to allow for retrospective registration of tomographic images with very different information content, the main emphasis being on sets of positron emission tomography images obtained with different tracers. A multivariate cost-function
Purpose: Stereotactic coordinate spaces and methods to adapt subjects to that space are required when performing averaging of functional studies across subjects. Methods: A rapid and fully automatic method to perform intersubject registration and adaptati
Entities such as object components, cavities, tunnels and concavities in 3D digital images can be useful in the framework of object analysis. For each object component, we first identify its convex deficiencies, by subtracting the object component from a covering polyhedron approximating the convex hull. Watershed segmentation is then used to decompose complex convex deficiencies into simpler parts, corresponding to individual cavities, concavities and tunnels of the object component. These entities are finally described by means of a representation system accounting for the shape features characterising them.
A robust segmentation and labelling method to identify individual ring shaped
Digital volume images can be created by assembling a stack of 2D images. By using a microtome for slicing, a Scanning Electron Microscope for imaging and digital analysis tools, we were able to create a small digital volume from a paper sample of Duplex-b
A detector for finding ring shaped objects occurring in clus-ters in 2D images with non-isotropic pixel dimensions have been developed. The rings are characterized as having a closed border and a void interior. We assume that the thick-ness of the rings s
When analysing fibres in paper using computerised image analysis applied to 3D i mages of paper, one measure of interest is the curvature along each individual fibre and how the curvature changes due to interaction with adjacent fibres. Starting from a cu
Segmentation of individual fibres in volume images is important when analysing the three dimensional (3D) fibre structure in paper and cellulose based composite materials. This paper presents a novel method for 3D tracking of individual fibres which can be used as a pre-segmentation step to a full cell wall segmentation or be used to estimate the fibre orientation. The tracking starts in one seed in each fibre and automatically extracts the local fibre orientation and the fibre centre point in each step using 3D information. Good results are obtained for cellulose fibres that are partially collapsed, cracked or irregularly shaped. The proposed method can also be used in other applications where tracking of tubular structures is of interest.
Fibre orientation is an important structural property of fibre-based materials. For example, in paper the orientation of the fibres influences the dimensional strength of the sheet and the tendency of the sheet to curl and twist at moisture changes. Here, we present a threedimensional image analysis method for estimating the fibre orientation and the orientation anisotropy. The proposed method can be applied directly to greyscale volume images and is based on local orientation estimates using quadrature filters and structure tensors. From the tensor field the fibre orientation can be estimated together with a corresponding certainty measurement. Good results are obtained for both synthetic fibre data sets and fibre based materials imaged using X-ray microtomography.
Pore structure characterisation of paper, using automated image analysis methods, has previously been performed in two-dimensional images. Three dimensional (3D) images have become available and thereby new representations and corresponding measurements are needed for 3D pore structure characterisation. In this article, we present a new pore structure representation, the individual pore-based skeleton, and new quantitative measurements for individual pores in 3D, such as surface area, orientation, anisotropy, and size distributions. We also present measurements for network relations, like tortuosity and connectivity. The data used to illustrate the pore structure representations and corresponding measurements are high resolution X-ray microtomography volume images of a layered duplex board imaged at the European Synchrotron Radiation Facility (ESRF). Quantification of the pore structure is exemplified and the results show that differences in pore structure between the layers in the cardboard can be characterised using the presented methods.
Ring artifacts can occur in reconstructed images from X-ray microtomography as full or partial circles centred on the rotation axis. In this paper, a 2D method is proposed that reduces these ring artifacts in the reconstructed images. The method consists of two main parts. First, the artifacts are localised in the image using local orientation estimation of the image structures and filtering to find ring patterns in the orientation information. Second, the map of the located artifacts is used to calculate a correction image using normalised convolution. The method is evaluated on 2D images from volume data of paper fibre imaged at the European Synchrotron Radiation Facility (ESRF) with high resolution X-ray microtomography. The results show that the proposed method reduces the artifacts and restores the pixel values for all types of partial and complete ring artifacts where the signal is not completely saturated.
A method for determining the water content at the interface between a press felt and a paper web has been developed. The water content was obtained by subtracting the estimated volume of the indented fibre web from the measured felt surface porosity of the press felt. The felt surface porosity was calculated from a topography map that was imaged with a Confocal Laser Scanning Microscope (CLSM) method. Here, the press felt was compressed against a smooth surface using a stress in the range of 0 to 10 MPa. Artefacts in the CLSM images were reduced using an image analysis method. The indentation of paper webs into the measured felt surface pores at different applied pressures was estimated using another image analysis method, simulating a rolling ball, with different radii of curvature for the different pressures and grammages, rolling over the felt surface. The ball radii were determined for a low and a high grammage web using the STFI-Packforsk Dewatering model. The method was evaluated in a case study with four press felts that had batt fibre diameters in a range between 22 and 78 μm. The indentation was calculated for webs with a low (15 g/m2) and a high grammage (105 g/m2), respectively. The evaluation showed that a considerable amount of porespace is available at the interface between the web and the felt. In most cases, the volume of the water-filled pores accounted for approximately 50% of the total surface porosity of the felt. Assuming a complete water saturation of the web/felt interface, approximately 10 g/m2 of water for the finest felt surface up to 40 g/m2 for the coarsest felt surface, could be located at the interface between the press felt and the paper web at a load of 10 MPa. This implies that a considerable amount of water is available for separation rewetting.
Fat distribution is an important criterium for meat quality evaluation and
In this work a computational approach for detecting and quantifying diabetic
In this paper we present an application to food science of image processing
The world of meat faces a permanent need for new methods of meat quality
Intramuscular fat content in meat influences some important meat quality
In this paper we present an image processing application for
In this paper we present a survey carried out to understand the choice of
The world of meat faces a permanent need for new methods of meat