Journal articles

1. BlobFinder, a tool for fluorescence microscopy image cytometry
   Authors: Amin Allalou, Carolina Wählby
   Journal: Computer Methods and Programs in Biomedicine 94(1), pp. 58-65
   Abstract: 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.

2. Structural characteristics of pore networks affecting print-through
   Authors: Gary Chinga-Carrasco (1), Maria Axelsson, Øyvind Eriksen (2), Stina Svensson
   (1) Norwegian Pulp and Paper Research Institute (PFI), Trondheim, Norway
   (2) Faculty of Natural Sciences and Technology, Norwegian University of Science and Technology, Norway
   Journal: Journal of Pulp and Paper Science (JPPS) 34(1), pp. 13-22
   Abstract: The pore structure of handsheets and of commercial newsprints is described in detail. The advantages and limitations of scanning electron microscopy and synchrotron radiation X-ray microtomography for pore-structure assessment are discussed. This gives insight into the two-dimensional and three-dimensional characteristics of the pore structure. A major achievement is the effective quantification of the submicron pores by scanning electron microscopy. It is demonstrated that submicron pores contribute positively to light scattering per unit thickness. The relationship between the pore structure, the light scattering and print-through is explored.

3. Estimation of pith position in untreated log ends in sawmill environments
   Authors: Kristin Norell, Gunilla Borgefors
   Journal: Computers and Electronics in Agriculture, 63(2), pp. 155-167
   Abstract: Two related methods for automatic estimation of the pith position, i.e., the centre of the annual rings, in wood log end face images are presented. We use images that depict untreated log end faces that are deliberately chosen to include difficulties such as rot, non-circular shape, uncentered pith and dirt. The images are taken with a regular digital camera in sawmill environments. Both presented methods use local orientation and Hough transform to detect the pith position, but two different ways to compute the local orientation are used. The results are promising for both methods. At least one of the methods is fast enough to use on-line at a sawmill.

4. A detailed analysis of 3D subcellular signal localization
   Authors: Amalka Pinidiyaarachchi, Agata Zieba (1), Amin Allalou, Katerina Pardali (1), Carolina Wählby
   (1) Dept. of Genetics and Pathology, UU
   Journal: Cytometry. Part A
   Abstract: Detection and localization of fluorescent signals in relation to other subcellular structures is an important task in various biological studies. Many methods for analysis of fluorescence microscopy image data are limited to 2D. As cells are in fact 3D structures, there is a growing need for robust methods for analysis of 3D data. This article presents an approach for detecting point-like fluorescent signals and analyzing their subnuclear position. Cell nuclei are delineated using marker-controlled (seeded) 3D watershed segmentation. User-defined object and background seeds are given as input, and gradient information defines merging and splitting criteria. Point-like signals are detected using a modified stable wave detector and localized in relation to the nuclear membrane using distance shells. The method was applied to a set of biological data studying the localization of Smad2-Smad4 protein complexes in relation to the nuclear membrane. Smad complexes appear as early as 1 min after stimulation while the highest signal concentration is observed 45 min after stimulation, followed by a concentration decrease. The robust 3D signal detection and concentration measures obtained using the proposed method agree with previous observations while also revealing new information regarding the complex formation.

5. Aspects on the reverse fuzzy distance transform
   Author: Stina Svensson
   Journal: Pattern Recognition Letters, 29(7), pp. 888-896
   Abstract: We extend the concept of the reverse distance transform for binary images to a fuzzy framework, leading to the reverse fuzzy distance transform. Furthermore, we introduce centres of maximal fuzzy balls intended for, e.g. fuzzy distance based skeletonization of a fuzzy object. Finally, we propose to use the reverse fuzzy distance transform as an alternative region growing process to the seeded watershed segmentation, in order to further emphasize the shape of fuzzy objects. We make a comparison using an application where the aim is to identify the cytoplasms in fluorescence microscopy images of cells.

6. Finding cells, finding molecules, finding patterns
   Authors: Carolina Wählby, Patrick Karlsson, Sara Henriksson (1), Chatarina Larsson (1), Mats Nilsson (1), Ewert Bengtsson
   (1) UU, Dept. of Genetics and Pathology, UU
   Journal: International Journal on Signal and Imaging Systems Engineering 1(1), pp. 11-17
   Abstract: Many modern molecular labeling techniques result in bright point signals. Signals from molecules that are detected directly inside a cell can be captured by fluorescence microscopy. Signals representing different types of molecules may be randomly distributed in the cells or show systematic patterns, indicating that the corresponding molecules have specific, non-random localisations and functions in the cell. Assessing this information requires high speed robust image segmentation followed by signal detection, and finally, pattern analysis. We present and discuss these types of methods and show an example of how the distribution of different variants of mitochondrial DNA can be analysed.