@inproceedings{PalmSchollLehmannetal., author = {Palm, Christoph and Scholl, Ingrid and Lehmann, Thomas M. and Spitzer, Klaus}, title = {Nutzung eines Farbkonstanz-Algorithmus zur Entfernung von Glanzlichtern in laryngoskopischen Bildern}, series = {Methoden der Medizinischen Informatik, Biometrie und Epidemiologie in der modernen Informationsgesellschaft}, booktitle = {Methoden der Medizinischen Informatik, Biometrie und Epidemiologie in der modernen Informationsgesellschaft}, editor = {Greiser, E. and Wischnewsky, M.}, publisher = {MMV Medien und Medizin}, address = {M{\"u}nchen}, isbn = {9783820813357}, pages = {300 -- 303}, abstract = {1 Einf{\"u}hrung Funktionelle und organische St{\"o}rungen im Larynx beeintr{\"a}chtigen die Ausdrucksf{\"a}higkeit des Menschen. Zur Diagnostik und Verlaufkontrolle werden die Stimmlippen im Larynx mit Hilfe der Video-Laryngoskopie aufgenommen. Zur optimalen Farbmessung wird dazu an das Lupenendoskop eine 3-Chip-CCD-Kamera angeschlossen, die eine unabh{\"a}ngige Aufnahme der drei Farbkan{\"a}le erlaubt. Die bisherige subjektive Befundung ist von der Erfahrung des Untersuchers abh{\"a}ngig und l{\"a}ßt nur eine grobe Klassifikation der Krankheitsbilder zu. Zur Objektivierung werden daher quantitative Parameter f{\"u}r Farbe, Textur und Schwingung entwickelt. Neben dem Einfluß der wechselnden Lichtquellenfarbe auf den Farbeindruck ist die Sekretauflage auf den Stimmlippen ein Problem bei der Farb-und Texturanalyse. Sie kann zu ausgedehnten Glanzlichtern f{\"u}hren und so weite Bereiche der Stimmlippen f{\"u}r die Farb-und Texturanalyse unbrauchbar machen. Dieser Beitrag stellt einen Farbkonstanz-Algorithmus vor, der unabh{\"a}ngig von der Lichtquelle quantitative Farbwerte des Gewebes liefert und die Glanzlichtdetektion und -elimination erm{\"o}glicht. 2 Methodik Ziel des Farbkonstanz-Algorithmus ist die Trennung von Lichtquellen-und Gewebefarbe. Unter Verwendung des dichromatischen Reflexionsmodells [1] kann die Oberfl{\"a}chenreflexion mit der Farbe der Lichtquelle und die K{\"o}rperreflexion mit der Gewebefarbe identifiziert werden. Der Farbeindruck entsteht aus der Linearkombination beider Farbkomponenten. Ihre Gewichtung ist von der Aufnahmegeometrie abh{\"a}ngig, insbesondere vom Winkel zwischen Oberfl{\"a}chennormalen und dem Positionsvektor der Lichtquelle. In einem zweistufigen Verfahren wird zun{\"a}chst die Lichtquellenfarbe gesch{\"a}tzt, dann die Gewebefarbe ermittelt. Hieraus k{\"o}nnen beide Farbanteile durch die Berechnung der Gewichtsfaktoren pixelweise getrennt werden.}, language = {de} } @article{Palm, author = {Palm, Christoph}, title = {Color Texture Classification by Integrative Co-Occurrence Matrices}, series = {Pattern Recognition}, volume = {37}, journal = {Pattern Recognition}, number = {5}, doi = {10.1016/j.patcog.2003.09.010}, pages = {965 -- 976}, abstract = {Integrative Co-occurrence matrices are introduced as novel features for color texture classification. The extended Co-occurrence notation allows the comparison between integrative and parallel color texture concepts. The information profit of the new matrices is shown quantitatively using the Kolmogorov distance and by extensive classification experiments on two datasets. Applying them to the RGB and the LUV color space the combined color and intensity textures are studied and the existence of intensity independent pure color patterns is demonstrated. The results are compared with two baselines: gray-scale texture analysis and color histogram analysis. The novel features improve the classification results up to 20\% and 32\% for the first and second baseline, respectively.}, language = {en} } @misc{GraesselAxerPalmetal., author = {Gr{\"a}ßel, David and Axer, Markus and Palm, Christoph and Dammers, J{\"u}rgen and Amunts, Katrin and Pietrzyk, Uwe and Zilles, Karl}, title = {Visualization of Fiber Tracts in the Postmortem Human Brain by Means of Polarized Light}, series = {NeuroImage}, volume = {47}, journal = {NeuroImage}, number = {Suppl. 1}, doi = {10.1016/S1053-8119(09)71415-6}, pages = {142}, subject = {Gehirn}, language = {en} } @article{PalmAxerGraesseletal., author = {Palm, Christoph and Axer, Markus and Gr{\"a}ßel, David and Dammers, J{\"u}rgen and Lindemeyer, Johannes and Zilles, Karl and Pietrzyk, Uwe and Amunts, Katrin}, title = {Towards ultra-high resolution fibre tract mapping of the human brain}, series = {Frontiers in Human Neuroscience}, volume = {4}, journal = {Frontiers in Human Neuroscience}, doi = {10.3389/neuro.09.009.2010}, pages = {9}, abstract = {Polarised light imaging (PLI) utilises the birefringence of the myelin sheaths in order to visualise the orientation of nerve fibres in microtome sections of adult human post-mortem brains at ultra-high spatial resolution. The preparation of post-mortem brains for PLI involves fixation, freezing and cutting into 100-μm-thick sections. Hence, geometrical distortions of histological sections are inevitable and have to be removed for 3D reconstruction and subsequent fibre tracking. We here present a processing pipeline for 3D reconstruction of these sections using PLI derived multimodal images of post-mortem brains. Blockface images of the brains were obtained during cutting; they serve as reference data for alignment and elimination of distortion artefacts. In addition to the spatial image transformation, fibre orientation vectors were reoriented using the transformation fields, which consider both affine and subsequent non-linear registration. The application of this registration and reorientation approach results in a smooth fibre vector field, which reflects brain morphology. PLI combined with 3D reconstruction and fibre tracking is a powerful tool for human brain mapping. It can also serve as an independent method for evaluating in vivo fibre tractography.}, subject = {Bildgebendes Verfahren}, language = {en} } @article{BeckerMatuschPalmetal., author = {Becker, Johanna Sabine and Matusch, Andreas and Palm, Christoph and Salber, Dagmar and Morton, Kathryn A. and Becker, Julia Susanne}, title = {Bioimaging of metals in brain tissue by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and metallomics}, series = {Metallomics}, journal = {Metallomics}, number = {2}, publisher = {Oxford Academic Press}, doi = {10.1039/b916722f}, pages = {104 -- 111}, abstract = {Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) has been developed and established as an emerging technique in the generation of quantitative images of metal distributions in thin tissue sections of brain samples (such as human, rat and mouse brain), with applications in research related to neurodegenerative disorders. A new analytical protocol is described which includes sample preparation by cryo-cutting of thin tissue sections and matrix-matched laboratory standards, mass spectrometric measurements, data acquisition, and quantitative analysis. Specific examples of the bioimaging of metal distributions in normal rodent brains are provided. Differences to the normal were assessed in a Parkinson's disease and a stroke brain model. Furthermore, changes during normal aging were studied. Powerful analytical techniques are also required for the determination and characterization of metal-containing proteins within a large pool of proteins, e.g., after denaturing or non-denaturing electrophoretic separation of proteins in one-dimensional and two-dimensional gels. LA-ICP-MS can be employed to detect metalloproteins in protein bands or spots separated after gel electrophoresis. MALDI-MS can then be used to identify specific metal-containing proteins in these bands or spots. The combination of these techniques is described in the second section.}, subject = {ICP-Massenspektrometrie}, language = {en} } @article{DammersAxerGraesseletal., author = {Dammers, J{\"u}rgen and Axer, Markus and Gr{\"a}ßel, David and Palm, Christoph and Zilles, Karl and Amunts, Katrin and Pietrzyk, Uwe}, title = {Signal enhancement in polarized light imaging by means of independent component analysis}, series = {NeuroImage}, volume = {49}, journal = {NeuroImage}, number = {2}, publisher = {Elsevier}, doi = {10.1016/j.neuroimage.2009.08.059}, pages = {1241 -- 1248}, abstract = {Polarized light imaging (PLI) enables the evaluation of fiber orientations in histological sections of human postmortem brains, with ultra-high spatial resolution. PLI is based on the birefringent properties of the myelin sheath of nerve fibers. As a result, the polarization state of light propagating through a rotating polarimeter is changed in such a way that the detected signal at each measurement unit of a charged-coupled device (CCD) camera describes a sinusoidal signal. Vectors of the fiber orientation defined by inclination and direction angles can then directly be derived from the optical signals employing PLI analysis. However, noise, light scatter and filter inhomogeneities interfere with the original sinusoidal PLI signals. We here introduce a novel method using independent component analysis (ICA) to decompose the PLI images into statistically independent component maps. After decomposition, gray and white matter structures can clearly be distinguished from noise and other artifacts. The signal enhancement after artifact rejection is quantitatively evaluated in 134 histological whole brain sections. Thus, the primary sinusoidal signals from polarized light imaging can be effectively restored after noise and artifact rejection utilizing ICA. Our method therefore contributes to the analysis of nerve fiber orientation in the human brain within a micrometer scale.}, subject = {Bildgebendes Verfahren}, language = {en} } @article{AxerAmuntsGraesseletal., author = {Axer, Markus and Amunts, Katrin and Gr{\"a}ßel, David and Palm, Christoph and Dammers, J{\"u}rgen and Axer, Hubertus and Pietrzyk, Uwe and Zilles, Karl}, title = {Novel Approach to the Human Connectome}, series = {NeuroImage}, volume = {54}, journal = {NeuroImage}, number = {2}, doi = {10.1016/j.neuroimage.2010.08.075}, pages = {1091 -- 1101}, abstract = {Signal transmission between different brain regions requires connecting fiber tracts, the structural basis of the human connectome. In contrast to animal brains, where a multitude of tract tracing methods can be used, magnetic resonance (MR)-based diffusion imaging is presently the only promising approach to study fiber tracts between specific human brain regions. However, this procedure has various inherent restrictions caused by its relatively low spatial resolution. Here, we introduce 3D-polarized light imaging (3D-PLI) to map the three-dimensional course of fiber tracts in the human brain with a resolution at a submillimeter scale based on a voxel size of 100 μm isotropic or less. 3D-PLI demonstrates nerve fibers by utilizing their intrinsic birefringence of myelin sheaths surrounding axons. This optical method enables the demonstration of 3D fiber orientations in serial microtome sections of entire human brains. Examples for the feasibility of this novel approach are given here. 3D-PLI enables the study of brain regions of intense fiber crossing in unprecedented detail, and provides an independent evaluation of fiber tracts derived from diffusion imaging data.}, subject = {Bildgebendes Verfahren}, language = {en} } @article{OsterholtSalberMatuschetal., author = {Osterholt, Tobias and Salber, Dagmar and Matusch, Andreas and Becker, Johanna Sabine and Palm, Christoph}, title = {IMAGENA: Image Generation and Analysis}, series = {International Journal of Mass Spectrometry}, volume = {307}, journal = {International Journal of Mass Spectrometry}, number = {1-3}, doi = {10.1016/j.ijms.2011.03.010}, pages = {232 -- 239}, abstract = {Metals are involved in many processes of life. They are needed for enzymatic reactions, are involved in healthy processes but also yield diseases if the metal homeostasis is disordered. Therefore, the interest to assess the spatial distribution of metals is rising in biomedical science. Imaging metal (and non-metal) isotopes by laser ablation mass spectrometry with inductively coupled plasma (LA-ICP-MS) requires a special software solution to process raw data obtained by scanning a sample line-by-line. As no software ready to use was available we developed an interactive software tool for Image Generation and Analysis (IMAGENA). Unless optimised for LA-ICP-MS, IMAGENA can handle other raw data as well. The general purpose was to reconstruct images from a continuous list of raw data points, to visualise these images, and to convert them into a commonly readable image file format that can be further analysed by standard image analysis software. The generation of the image starts with loading a text file that holds a data column of every measured isotope. Specifying general spatial domain settings like the data offset and the image dimensions is done by the user getting a direct feedback by means of a preview image. IMAGENA provides tools for calibration and to correct for a signal drift in the y-direction. Images are visualised in greyscale as well a pseudo-colours with possibilities for contrast enhancement. Image analysis is performed in terms of smoothed line plots in row and column direction.}, subject = {ICP-Massenspektrometrie}, language = {en} } @article{BeckerMatuschBeckeretal., author = {Becker, Johanna Sabine and Matusch, Andreas and Becker, Julia Susanne and Wu, Bei and Palm, Christoph and Becker, Albert Johann and Salber, Dagmar}, title = {Mass spectrometric imaging (MSI) of metals using advanced BrainMet techniques for biomedical research}, series = {International Journal of Mass Spectrometry}, volume = {307}, journal = {International Journal of Mass Spectrometry}, number = {1-3}, publisher = {eLSEVIER}, address = {Elsevier}, doi = {10.1016/j.ijms.2011.01.015}, pages = {3 -- 15}, abstract = {Mass spectrometric imaging (MSI) is a young innovative analytical technique and combines different fields of advanced mass spectrometry and biomedical research with the aim to provide maps of elements and molecules, complexes or fragments. Especially essential metals such as zinc, copper, iron and manganese play a functional role in signaling, metabolism and homeostasis of the cell. Due to the high degree of spatial organization of metals in biological systems their distribution analysis is of key interest in life sciences. We have developed analytical techniques termed BrainMet using laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) imaging to measure the distribution of trace metals in biological tissues for biomedical research and feasibility studies—including bioaccumulation and bioavailability studies, ecological risk assessment and toxicity studies in humans and other organisms. The analytical BrainMet techniques provide quantitative images of metal distributions in brain tissue slices which can be combined with other imaging modalities such as photomicrography of native or processed tissue (histochemistry, immunostaining) and autoradiography or with in vivo techniques such as positron emission tomography or magnetic resonance tomography. Prospective and instrumental developments will be discussed concerning the development of the metalloprotein microscopy using a laser microdissection (LMD) apparatus for specific sample introduction into an inductively coupled plasma mass spectrometer (LMD-ICP-MS) or an application of the near field effect in LA-ICP-MS (NF-LA-ICP-MS). These nano-scale mass spectrometric techniques provide improved spatial resolution down to the single cell level.}, subject = {Massenspektrometrie}, language = {en} } @article{KolevKirchgessnerHoubenetal., author = {Kolev, Kalin and Kirchgeßner, Norbert and Houben, Sebastian and Csisz{\´a}r, Agnes and Rubner, Wolfgang and Palm, Christoph and Eiben, Bj{\"o}rn and Merkel, Rudolf and Cremers, Daniel}, title = {A variational approach to vesicle membrane reconstruction from fluorescence imaging}, series = {Pattern Recognition}, volume = {44}, journal = {Pattern Recognition}, number = {12}, publisher = {Elsevier}, doi = {10.1016/j.patcog.2011.04.019}, pages = {2944 -- 2958}, abstract = {Biological applications like vesicle membrane analysis involve the precise segmentation of 3D structures in noisy volumetric data, obtained by techniques like magnetic resonance imaging (MRI) or laser scanning microscopy (LSM). Dealing with such data is a challenging task and requires robust and accurate segmentation methods. In this article, we propose a novel energy model for 3D segmentation fusing various cues like regional intensity subdivision, edge alignment and orientation information. The uniqueness of the approach consists in the definition of a new anisotropic regularizer, which accounts for the unbalanced slicing of the measured volume data, and the generalization of an efficient numerical scheme for solving the arising minimization problem, based on linearization and fixed-point iteration. We show how the proposed energy model can be optimized globally by making use of recent continuous convex relaxation techniques. The accuracy and robustness of the presented approach are demonstrated by evaluating it on multiple real data sets and comparing it to alternative segmentation methods based on level sets. Although the proposed model is designed with focus on the particular application at hand, it is general enough to be applied to a variety of different segmentation tasks.}, subject = {Dreidimensionale Bildverarbeitung}, language = {en} }