According to the founding documents, the objective of the CBA is ``to create the know-how needed for an operative and sensible use of digital image analysis in society, particularly in the fields of environment and medicine.'' Traditionally, the research has been more or less organized in three groups, led by Prof. Ewert Bengtsson, Prof. Gunilla Borgefors, and Doc. Tommy Lindell. However, the borders between the groups have become more and more fuzzy, sometimes non-existent. This is a development we encourage, the goal being to create as much high quality research as possible not to maintain organizational structure. Also, and new configurations have appeared and old are disappearing. The group on aquatic remote sensing led by Lindell is decreasing since Lindell has retired and is only working part time. We have unfortunately not been able to find support for a new position to continue work in this field. Instead, a new group on graphics and visualization, which nicely complements our 3D image analysis work, has been added. Prof. Stefan Seipel, recruited in 2002, works 20% of his time at CBA. This year, new Associate Prof. (lecturer) in visualization, Doc. Ingela Nyström, was recruited. In addition, we recruited a new Assistant Prof., Carolina Wählby, who received her PhD at CBA in October 2003. The other seniors involved in research are Prof. Fredrik Bergholm, Assistant Prof. Stina Svensson, and Dr. Bo Nordin.
Other welcome additions to the group, adding a new international dimension to our work, are two new ``sandwich" PhD students from Sri Lanka that will spend about half of each year at CBA and half at their home universities. We already have a similar arrangement with one student from Novi Sad, Serbia. We also recruited two ``normal" PhD students.
From this year, we do not divide this summary according to ``the groups". The order of main activities below follow that in Section 5.1, which is arbitrary (even though similar projects are grouped).
For a number of years we have been working on wood fibre applications, both fibres in the wood and in paper. The ultimate goal is to understand how individual fibres build up paper and what effect different types of fibre networks have on paper properties. This year, a new PhD student, Maria Axelsson, was engaged to continue the investigations of the 3D structure of paper and board. Svensson and Sintorn has looked at the pore structure of board. Also, there have been no less than five Master Thesis on various aspects on paper, in co-operation with StoraEnso or STFI-Packforsk.
Forest inventory from air-borne sensors have been an active and productive research field in the group since its beginning in 1994. The aim is to make inventory from such data so detailed and correct that it can replace most field inventories. This year, Mats Erikson defended his thesis on tree crown and tree species classification in color infrared high resolution aerial images. On the stand level, classification is 95% correct, when distinguishing between the four most common species in Sweden: spruce, pine, birch, and aspen.
Pathology in plants can be detected early using hyperspectral data. We have used our expertise on extracting information from hyperspectral data for judging disease severity in wheat, in a co-operation between PhD students Hamed Hamid Mohammed and Anders Larsolle at Dept. of Biometry and Engineering, SLU, Uppsala.
We believe image analysis can provide some of the key tools for understanding biology at all levels of resolution from the molecular via the intra- and inter-cellular, tissue organizational, and up to the organ and organism levels. We have projects at almost all those levels, seeking to develop the new tools and methods needed.
On the molecular level we have two projects. PhD student Ida-Maria Sintorn and Stina Svensson are working on segmentation in 3D based on both geometry and grey-level values, and applying the methods to Sidec Electron Tomography (SET) images of protein molecules. The goal is to find possible proteins in very noisy images. Patrick Karlsson and Carolina Wählby, in collaboration with Dept. of Genetics and Pathology, UU, studied how the small 3D ``blobs" created by the imaging system from signals from a few molecules, i.e. far below optical resolution, can be resolved to give good quantitative data about the distributions of the different labeled molecules.
Sintorn has also, together with Dept. of Medicine, Karolinska Institute, been involved in the identification and classification of human cytomegalovirus cpaids in noisy transmission electron microscopy images. This work won an innovation prize 2004.
On the cellular level, we have developed ways of segmenting and tracking the development of individual cells over time in time lapse photography sequences of cell cultures. This work has been carried out in collaboration with Dept. of Signals and Systems, Chalmers University of Technology and Dept. of Clinical Neuroscience, Göteborg University. The new PhD students Magnus Gedda and Sri Lankan Amalka Pinidiyaarachchi has been doing most of this work together with Karlsson, Wählby and Bengtsson. Also, a Chinese visiting student ``April" Tang Chunming contributed by developing a prototype tracking program.
Wählby and Sintorn has also worked on segmentation of various sub-cellular structures, in co-operation with Dept. of Oncology/Pathology, Karolinska Institute. Immunostaining and fluorescence microscopy is used, and the goal is to understand the 3D organization of normal and pathological cell nuclei.
On the organ level, PhD student Xavier Tizon has investigated the uses of grey-level connectivity and fuzzy set theory for use in, mainly, Magnetic Resonance Angiography (MRA) images. One application is arteries-veins separation, in co-operation with Dept. of Medicine and Care, Linköping University. The main activity this year was project where the task is analysis of the main artery tree in whole-body MRI. Minimal user interaction should be necessary for segmentation. After segmentation, measures for a total plaque burden were developed. The methods are aimed at massive scanning programmes for early detection of arteriosclerosis. This work is done in close co-operation with Dept. of Oncology, Radiology, and Clinical Immunology, UU Hospital. Tizon defended his thesis in Oct. 2004.
PhD student Pascha Razifar is also working on organ level images, studying the statistical properties of Positron Emission Tomography (PET) images. He is developing better ways of modeling the imaging process and of extracting relevant parameters. This work is done in close collaboration with Imanet AB, Uppsala.
Also on the organ level is the work we do using haptics. Haptics use the sense of touch, via a force feedback probe, in addition to stereo vision. Erik Vidholm and the other Sri Lankan student, Suthakar Somaskandan, are the PhD students doing this work. We are developing new ways for interacting with 3D images, mainly from magnetic resonance imaging (MRI). The first result was a method for improved interaction with the MRA images from Tizon's work. The group has now moved on to study liver segmentation issues. As visualization is important for the haptic projects, Nyström is closely involved. This year, we also had a master thesis project, in which a good tool for object manipulation and visualization was developed.
During the last quarter of the year Bengtsson was on sabbatical at University of Queensland, Brisbane, Australia, that will last until March 2005. He chose this host for his sabbatical because they are one of the more active groups in one of his long standing areas of interest, the automated screening of cell preparations for early detection of cervical cancer. The host researchers are also very much interested in analysis of magnetic resonance time sequence images of breasts for accurate cancer diagnosis, which ties in very well with the methods development for 3D and 4D image analysis CBA. Therefore, so most of the work during Bengtsson's stay in Brisbane has been on the latter problem. This collaboration will likely continue after Bengtsson's return to Uppsala.
In addition to the application oriented image analysis work described above, we also develop new, general, image analysis methods, especially for volume (and higher dimensional) images and hyperspectral data.
PhD student Felix Wehrmann has explored a number of different ways of expressing general shape, without relying on landmarks. He has come to the conclusion that a special kind of neural networks offers interesting new possibilities. Bergholm has worked together with Wehrmann, who presented his thesis in May 2004.
Four PhD students are jointly advised by Prof. Christer Kiselman, Dept. of Mathematics, UU and Borgefors. Two are placed at CBA, the others at Dept. of Mathematics. PhD student Ola Weistrand aims to develop global shape descriptions for volume objects, using linear combinations of spherical harmonics. First, the object boundary is mapped onto a sphere using harmonic functions. This leads to distortions, that make immediate application of spherical harmonics impossible. This year, the work has been concentrated on removing or alleviating these distortions.
Robin Strand is the other joint PhD student at CBA. He is funded by the Graduate School in Mathematics and Computing at UU. Strand develops image processing tool for volume images digitized in the bcc and fcc grids (where voxels are not cubes, but ``rounder" polyhedra). He developed distance transforms, resolution pyramids, and skeletonization algorithms for these grids.
We are particularly interested in finding ways of registering images with many channels and to analyze such images. This is usually called imaging spectrometry. Fredrik Bergholm and PhD student Hamed Hamid Mohammed has developed a new concept for a color mosaic sensor which has led to a patent application. Hamid Muhammad has also developed new ways of normalizing and interpreting the hyperspectral information using independent component analysis and neural networks techniques.
Serbian PhD student Nataša Sladoje is working on fuzzy shape analysis in 2D and 3D. This means development of shape analysis directly in grey-level images or in fuzzy segmented images. Work has concentrated on precise area and volume measurements, shape moments, and analysis of shape signatures. This work is partly done in co-operation with Dept. of Radiology, University of Pennsylvania, Philadelphia, USA, and INPG, Grenoble, France.
Our long-time co-operation with Istituto di Cibernetica, ``E. Caianiello", CNR, Pozzuoli, Italy, continues. Involved from CBA are mainly Borgefors, Nyström and Svensson. We have long worked on digital distance transforms, decompositions, and skeletons (in 2D, 3D, 4D), and recently on using binary methods in 3D to accomplish various 2D grey-level image methods. We have also this year written a number book chapters on our pet subjects - distance transforms and skeletons - that will be published 2005 (or later).
Our graphics and visualization research is still not very extensive, but a number of projects are being pursued. In fact, even before we officially had positions for graphics and visualization we have been active in that field. A result of that is the thesis by Anders Hast from Gävle University College, who, together with Tony Barrera, has been studying how various image rendering algorithms can be implemented more efficiently. The work has resulted in several publications describing how shading and bump mapping algorithms can be significantly improved. Hast defended his thesis in April 2004.
Stefan Seipel is working mainly at University College of Gävle, but 20% of his time with us. One of his two main projects is efficient visualization of forest data. The visualization includes synthesizing detailed vegetation and animating it. Animation is essential for generating visual clues. The models are aimed for long-term forest planning and education. The other main project is to research new methods for visualizing data efficiently for a group of people who interact in the same physical environment. This project is done in co-operation with the Swedish Defence College.
Somaskandan and Nyström are developing techniques for exploration of 3D medical images for visualization on standard PC hardware. Earlier, interactive techniques required very expensive computers, but today a PC with a standard graphics card, developed for the game market, could be used.
Aquatic remote sensing has been a strong and active research topic at CBA from its beginning, but is now, sadly, soon coming to an end. However, there are still a number of projects going on. Activities vary from mapping and monitoring of algae blooms and distribution of plumes in lakes to mapping and monitoring of tropical coasts and sea bottoms.
Lindell and Philipson have continued co-operation with the Italian groups from our earlier EU project in ROSALMA, monitoring of chlorophyll and macrophytes from satellites; and in NYMPHA, experimentation on a remote sensing integrated system for lake water monitoring. This project has also involved NIVA, Norway in field work and in applying MERIS data to the developed techniques from imaging spectrometry.
The co-operation with NIVA was extended to a new project on arctic and sub-arctic conditions, headed by Bergholm.
Lindell and Philipson have, together with the Swedish Environmental Protection Agency, classified the habitats along the entire Swedish coast using Landsat-7 imagery.
An important aspect of our theoretical work is applying linear transformations methods, based on such as ICA (Independent Component Analysis) to hyper spectral images of Swedish lake waters. This research is mainly performed by PhD student Hamid Mohammed.
Lindell and Philipson have also continued the development of image analysis methods for imaging spectrometry. The long-term goal here is using satellite, together with airborne hyperspectral data, for different environmental applications. For some years, the work has focused on the detection of coral bleaching from remote sensing sources.
Finally, PhD student Julia Åhlén from University College Gävle has developed ways of correcting images taking with standard digital cameras under water for the loss of light with longer wavelengths with increasing depth. Her work can be important for many applications, such as marine biology and underwater archaeology. Her work won an award at the Swedish image analysis symposium this year, for being most relevant for industry.
Our image analysis platform IMP which has been used for many years in our research projects and in our courses is now approaching retirement and a new generation software, named PIXY, has been launched. There are, however, many things tied to the old system so the transition will likely take a number of years. Both systems have been designed and implemented by Bo Nordin.
CBA has also supervised as many as eleven Master Theses that were completed this year, seven of them with industrial co-operation partners. The theses treated: A general image analysis system; Finding cow teats for automatic milking; Analyzing fibre orientation in paper; Classification of usefulness of images of fluorescent molecules; Analyzing layering in stratified paper; Registration of 3D images of rats from computer tomography, magnetic resonance, and PET images; Segmenting the pulp layers in cross-section images of paper board; Automatic acquisition of cross-section images of paper in a scanning electron microscope; Real time surface rendering for our haptic environment; Visualization of the 3D fibre structure of paper; and Determining bark content in wood-chips for pulping.