@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} } @inproceedings{PalmPietrzyk, author = {Palm, Christoph and Pietrzyk, Uwe}, title = {Time-Dependent Joint Probability Speed Function for Level-Set Segmentation of Rat-Brain Slices}, series = {Proceedings of the SPIE Medical Imaging 6914: Image Processing 69143U}, booktitle = {Proceedings of the SPIE Medical Imaging 6914: Image Processing 69143U}, number = {6914}, doi = {10.1117/12.770673}, pages = {69143U-1 -- 69143U-8}, abstract = {The segmentation of rat brain slices suffers from illumination inhomogeneities and staining effects. State-of-the-art level-set methods model slice and background with intensity mixture densities defining the speed function as difference between the respective probabilites. Nevertheless, the overlap of these distributions causes an inaccurate stopping at the slice border. In this work, we propose the characterisation of the border area with intensity pairs for inside and outside estimating joint intensity probabilities. Method - In contrast to global object and background models, we focus on the object border characterised by a joint mixture density. This specifies the probability of the occurance of an inside and an outside value in direct adjacency. These values are not known beforehand, because inside and outside depend on the level-set evolution and change during time. Therefore, the speed function is computed time-dependently at the position of the current zero level-set. Along this zero level-set curve, the inside and outside values are derived as mean along the curvature normal directing inside and outside the object. Advantage of the joint probability distribution is to resolve the distribution overlaps, because these are assumed to be not located at the same border position. Results - The novel time-dependent joint probability based speed function is compared expermimentally with single probability based speed functions. Two rat brains with about 40 slices are segmented and the results analysed using manual segmentations and the Tanimoto overlap measure. Improved results are recognised for both data sets.}, subject = {Kernspintomografie}, language = {en} } @inproceedings{SchubertPietrzykReisseletal., author = {Schubert, Nicole and Pietrzyk, Uwe and Reißel, Martin and Palm, Christoph}, title = {Reduktion von Rissartefakten durch nicht-lineare Registrierung in histologischen Schnittbildern}, series = {Bildverarbeitung f{\"u}r die Medizin 2009; Algorithmen - Systeme - Anwendungen; Proceedings des Workshops vom 22. bis 25. M{\"a}rz 2009 in Heidelberg}, booktitle = {Bildverarbeitung f{\"u}r die Medizin 2009; Algorithmen - Systeme - Anwendungen; Proceedings des Workshops vom 22. bis 25. M{\"a}rz 2009 in Heidelberg}, publisher = {Springer}, address = {Berlin}, pages = {410 -- 414}, abstract = {In dieser Arbeit wird ein Verfahren vorgestellt, das Rissartefakte, die in histologischen Rattenhirnschnitten vorkommen k{\"o}nnen, durch nicht-lineare Registrierung reduziert. Um die Optimierung in der Rissregion zu leiten, wird der Curvature Registrierungsansatz um eine Metrik basierend auf der Segmentierung der Bilder erweitert. Dabei erzielten Registrierungen mit der ausschließlichen Segmentierung des Risses bessere Ergebnisse als Registrierungen mit einer Segmentierung des gesamten Hirnschnitts. Insgesamt zeigt sich eine deutliche Verbesserung in der Rissregion, wobei der verbleibende reduzierte Riss auf die Glattheitsbedingungen des Regularisierers zur{\"u}ckzuf{\"u}hren ist.}, subject = {Registrierung }, language = {de} } @article{BeckerZoriyMatuschetal., author = {Becker, Johanna Sabine and Zoriy, Miroslav and Matusch, Andreas and Wu, Bei and Salber, Dagmar and Palm, Christoph and Becker, Julia Susanne}, title = {Bioimaging of Metals by Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS)}, series = {Mass Spectrometry Reviews}, volume = {29}, journal = {Mass Spectrometry Reviews}, doi = {10.1002/mas.20239}, pages = {156 -- 175}, abstract = {The distribution analysis of (essential, beneficial, or toxic) metals (e.g., Cu, Fe, Zn, Pb, and others), metalloids, and non-metals in biological tissues is of key interest in life science. Over the past few years, the development and application of several imaging mass spectrometric techniques has been rapidly growing in biology and medicine. Especially, in brain research metalloproteins are in the focus of targeted therapy approaches of neurodegenerative diseases such as Alzheimer's and Parkinson's disease, or stroke, or tumor growth. Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) using double-focusing sector field (LA-ICP-SFMS) or quadrupole-based mass spectrometers (LA-ICP-QMS) has been successfully applied as a powerful imaging (mapping) technique to produce quantitative images of detailed regionally specific element distributions in thin tissue sections of human or rodent brain. Imaging LA-ICP-QMS was also applied to investigate metal distributions in plant and animal sections to study, for example, the uptake and transport of nutrient and toxic elements or environmental contamination. The combination of imaging LA-ICP-MS of metals with proteomic studies using biomolecular mass spectrometry identifies metal-containing proteins and also phosphoproteins. Metal-containing proteins were imaged in a two-dimensional gel after electrophoretic separation of proteins (SDS or Blue Native PAGE). Recent progress in LA-ICP-MS imaging as a stand-alone technique and in combination with MALDI/ESI-MS for selected life science applications is summarized.}, subject = {Bildgebendes Verfahren}, language = {en} } @article{IlgnerPalmSchuetzetal., author = {Ilgner, Justus F. R. and Palm, Christoph and Sch{\"u}tz, Andreas G. and Spitzer, Klaus and Westhofen, Martin and Lehmann, Thomas M.}, title = {Colour Texture Analysis for Quantitative Laryngoscopy}, series = {Acta Otolaryngologica}, volume = {123}, journal = {Acta Otolaryngologica}, doi = {10.1080/00016480310000412}, pages = {730 -- 734}, abstract = {Whilst considerable progress has been made in enhancing the quality of indirect laryngoscopy and image processing, the evaluation of clinical findings is still based on the clinician's judgement. The aim of this paper was to examine the feasibility of an objective computer-based method for evaluating laryngeal disease. Digitally recorded images obtained by 90 degree- and 70 degree-angled indirect rod laryngoscopy using standardized white balance values were made of 16 patients and 19 healthy subjects. The digital images were evaluated manually by the clinician based on a standardized questionnaire, and suspect lesions were marked and classified on the image. Following colour separation, normal vocal cord areas as well as suspect lesions were analyzed automatically using co-occurrence matrices, which compare colour differences between neighbouring pixels over a predefined distance. Whilst colour histograms did not provide sufficient information for distinguishing between healthy and diseased tissues, consideration of the blue content of neighbouring pixels enabled a correct classification in 81.4\% of cases. If all colour channels (red, green and blue) were regarded simultaneously, the best classification correctness obtained was 77.1\%. Although only a very basic classification differentiating between healthy and diseased tissue was attempted, the results showed progress compared to grey-scale histograms, which have been evaluated before. The results document a first step towards an objective, machine-based classification of laryngeal images, which could provide the basis for further development of an expert system for use in indirect laryngoscopy.}, language = {en} } @article{PalmVietenSalberetal., author = {Palm, Christoph and Vieten, Andrea and Salber, Dagmar and Pietrzyk, Uwe}, title = {Evaluation of Registration Strategies for Multi-modality Images of Rat Brain Slices}, series = {Physics in Medicine and Biology}, volume = {54}, journal = {Physics in Medicine and Biology}, number = {10}, doi = {10.1088/0031-9155/54/10/021}, pages = {3269 -- 3289}, abstract = {In neuroscience, small-animal studies frequently involve dealing with series of images from multiple modalities such as histology and autoradiography. The consistent and bias-free restacking of multi-modality image series is obligatory as a starting point for subsequent non-rigid registration procedures and for quantitative comparisons with positron emission tomography (PET) and other in vivo data. Up to now, consistency between 2D slices without cross validation using an inherent 3D modality is frequently presumed to be close to the true morphology due to the smooth appearance of the contours of anatomical structures. However, in multi-modality stacks consistency is difficult to assess. In this work, consistency is defined in terms of smoothness of neighboring slices within a single modality and between different modalities. Registration bias denotes the distortion of the registered stack in comparison to the true 3D morphology and shape. Based on these metrics, different restacking strategies of multi-modality rat brain slices are experimentally evaluated. Experiments based on MRI-simulated and real dual-tracer autoradiograms reveal a clear bias of the restacked volume despite quantitatively high consistency and qualitatively smooth brain structures. However, different registration strategies yield different inter-consistency metrics. If no genuine 3D modality is available, the use of the so-called SOP (slice-order preferred) or MOSOP (modality-and-slice-order preferred) strategy is recommended.}, subject = {Histologie}, language = {en} } @inproceedings{EibenPalmPietrzyketal., author = {Eiben, Bj{\"o}rn and Palm, Christoph and Pietrzyk, Uwe and Davatzikos, Christos and Amunts, Katrin}, title = {Error Correction using Registration for Blockface Volume Reconstruction of Serial Histological Sections of the Human Brain}, series = {Bildverarbeitung f{\"u}r die Medizin 2010; Algorithmen - Systeme - Anwendungen ; Proceedings des Workshops vom 22. bis 25. M{\"a}rz 2009 in Heidelberg}, booktitle = {Bildverarbeitung f{\"u}r die Medizin 2010; Algorithmen - Systeme - Anwendungen ; Proceedings des Workshops vom 22. bis 25. M{\"a}rz 2009 in Heidelberg}, publisher = {Springer}, address = {Berlin}, pages = {301 -- 305}, abstract = {For accurate registration of histological sections blockface images are frequently used as three dimensional reference. However, due to the use of endocentric lenses the images suffer from perspective errors such as scaling and seemingly relative movement of planes which are located in different distances parallel to the imaging sensor. The suggested correction of those errors is based on the estimation of scaling factors derived from image registration of regions characterized by differing distances to the point of view in neighboring sections. The correction allows the generation of a consistent three dimensional blockface volume.}, subject = {Histologie}, language = {en} } @misc{BeyerWeigertPalmetal., author = {Beyer, Thomas and Weigert, Markus and Palm, Christoph and Quick, Harald H. and M{\"u}ller, Stefan P. and Pietrzyk, Uwe and Vogt, Florian and Martinez, M.J. and Bockisch, Andreas}, title = {Towards MR-based attenuation correction for whole-body PET/MR imaging}, series = {The Journal of Nuclear Medicine}, volume = {47}, journal = {The Journal of Nuclear Medicine}, number = {Suppl. 1}, pages = {384P}, subject = {Kernspintomografie}, 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} } @misc{WeigertBeyerQuicketal., author = {Weigert, Markus and Beyer, Thomas and Quick, Harald H. and Pietrzyk, Uwe and Palm, Christoph and M{\"u}ller, Stefan P.}, title = {Generation of a MRI reference data set for the validation of automatic, non-rigid image co-registration algorithms}, series = {Nuklearmedizin}, volume = {46}, journal = {Nuklearmedizin}, number = {2}, pages = {A116}, subject = {Kernspintomografie}, language = {en} } @inproceedings{PietrzykBauerVietenetal., author = {Pietrzyk, Uwe and Bauer, Dagmar and Vieten, Andrea and Bauer, Andreas and Langen, Karl-Josef and Zilles, Karl and Palm, Christoph}, title = {Creating consistent 3D multi-modality data sets from autoradiographic and histological images of the rat brain}, series = {IEEE Nuclear Science Symposium Conference Record}, volume = {6}, booktitle = {IEEE Nuclear Science Symposium Conference Record}, doi = {10.1109/NSSMIC.2004.1466754}, pages = {4001 -- 4003}, abstract = {Volumetric representations of autoradiographic and histological images gain ever more interest as a base to interpret data obtained with /spl mu/-imaging devices like microPET. Beyond supporting spatial orientation within rat brains especially autoradiographic images may serve as a base to quantitatively evaluate the complex uptake patterns of microPET studies with receptor ligands or tumor tracers. They may also serve for the development of rat brain atlases or data models, which can be explored during further image analysis or simulation studies. In all cases a consistent spatial representation of the rat brain, i.e. its anatomy and the corresponding quantitative uptake pattern, is required. This includes both, a restacking of the individual two-dimensional images and the exact registration of the respective volumes. We propose strategies how these volumes can be created in a consistent way and trying to limit the requirements on the circumstances during data acquisition, i.e. being independent from other sources like video imaging of the block face prior to cutting or high resolution micro-X-ray CT or micro MRI.}, language = {en} }