TY - JOUR A1 - Ott, Tankred A1 - Palm, Christoph A1 - Vogt, Robert A1 - Oberprieler, Christoph T1 - GinJinn: An object-detection pipeline for automated feature extraction from herbarium specimens JF - Applications in Plant Sciences N2 - PREMISE: The generation of morphological data in evolutionary, taxonomic, and ecological studies of plants using herbarium material has traditionally been a labor-intensive task. Recent progress in machine learning using deep artificial neural networks (deep learning) for image classification and object detection has facilitated the establishment of a pipeline for the automatic recognition and extraction of relevant structures in images of herbarium specimens. METHODS AND RESULTS: We implemented an extendable pipeline based on state-of-the-art deep-learning object-detection methods to collect leaf images from herbarium specimens of two species of the genus Leucanthemum. Using 183 specimens as the training data set, our pipeline extracted one or more intact leaves in 95% of the 61 test images. CONCLUSIONS: We establish GinJinn as a deep-learning object-detection tool for the automatic recognition and extraction of individual leaves or other structures from herbarium specimens. Our pipeline offers greater flexibility and a lower entrance barrier than previous image-processing approaches based on hand-crafted features. KW - Deep Learning KW - herbarium specimens KW - object detection KW - visual recognition KW - Deep Learning KW - Objekterkennung KW - Maschinelles Sehen KW - Pflanzen Y1 - 2020 U6 - https://doi.org/10.1002/aps3.11351 SN - 2168-0450 VL - 8 IS - 6 SP - e11351 PB - Wiley, Botanical Society of America ER - TY - CHAP A1 - Palm, Christoph A1 - Keysers, Daniel A1 - Lehmann, Thomas M. A1 - Spitzer, Klaus T1 - Gabor Filtering of Complex Hue/Saturation Images for Color Texture Classification T2 - Proceedings of the 5th Joint Conference on Information Science (JCIS) 2, The Association for Intelligent Machinery, Atlantic City, NJ, 2000 N2 - Objective: Complex hue/saturation images as a new approach for color texture classification using Gabor filters are introduced and compared with common techniques. Method: The interpretation of hue and saturationas polar coordinates allows direct use of the HSV-colorspace for Fourier transform. This technique is applied for Gabor feature extraction of color textures. In contrast to other color features based on the RGB-colorspace [1] the combination of color bands is done previous to the filtering. Results: The performance of the new HS-featuresis compared with that of RGB based as well as grayscale Gabor features by evaluating the classifi-cation of 30 natural textures. The new HS-featuresshow same results like the best RGB features but allow a more compact representation. On the averagethe color features improve the results of grayscale features. Conclusion: The consideration of the color information enhances the classification of color texture. The choice of colorspace cannot be adjudged finally, but the introduced features suggest the use of the HSV-colorspace with less features than RGB. Y1 - 2000 UR - http://www.keysers.net/daniel/files/JCIS2000_palm.pdf SP - 45 EP - 49 ER - TY - CHAP A1 - Eiben, Björn A1 - Palm, Christoph A1 - Pietrzyk, Uwe A1 - Davatzikos, Christos A1 - Amunts, Katrin T1 - Error Correction using Registration for Blockface Volume Reconstruction of Serial Histological Sections of the Human Brain T2 - Bildverarbeitung für die Medizin 2010; Algorithmen - Systeme - Anwendungen ; Proceedings des Workshops vom 22. bis 25. März 2009 in Heidelberg N2 - 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. KW - Histologie KW - Diagnostik KW - Bildgebendes Verfahren KW - Schnittdarstellung KW - Fehlerbehandlung Y1 - 2010 UR - http://ceur-ws.org/Vol-574/bvm2010_61.pdf SP - 301 EP - 305 PB - Springer CY - Berlin ER - TY - CHAP A1 - Scholl, Ingrid A1 - Palm, Christoph A1 - Sovakar, Abhijit A1 - Lehmann, Thomas M. A1 - Spitzer, Klaus ED - Arnolds, B. ED - Mueller, H. ED - Saupe, D. ED - Tolxdorff, Thomas T1 - Quantitative Analyse der Stimmlippen T2 - 5. Workshop Digitale Bildverarbeitung in der Medizin, Universität Freiburg, 10.-11. März 1997 KW - Konturverfolgung KW - Snakes KW - Farbanalyse KW - Dichromatisches Reflexionsmodell KW - Farbkonstanz KW - Laryngoskopie Y1 - 1997 UR - https://pdfs.semanticscholar.org/9a0c/9e7dc883ccf6e8a8a686c28422238adb5f35.pdf SP - 81 EP - 86 ER - TY - JOUR A1 - Ilgner, Justus F. R. A1 - Palm, Christoph A1 - Schütz, Andreas G. A1 - Spitzer, Klaus A1 - Westhofen, Martin A1 - Lehmann, Thomas M. T1 - Colour Texture Analysis for Quantitative Laryngoscopy JF - Acta Otolaryngologica N2 - 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. KW - diagnostic laryngoscopy KW - electronic imaging KW - endoscopy KW - neoplastic larynx disease Y1 - 2003 U6 - https://doi.org/10.1080/00016480310000412 VL - 123 SP - 730 EP - 734 ER - TY - JOUR A1 - Becker, Johanna Sabine A1 - Matusch, Andreas A1 - Palm, Christoph A1 - Salber, Dagmar A1 - Morton, Kathryn A. A1 - Becker, Julia Susanne T1 - Bioimaging of metals in brain tissue by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and metallomics JF - Metallomics N2 - 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. KW - ICP-Massenspektrometrie KW - Metalle KW - Metallproteide KW - Elektrophorese KW - Gehirn Y1 - 2010 U6 - https://doi.org/10.1039/b916722f IS - 2 SP - 104 EP - 111 PB - Oxford Academic Press ER - TY - CHAP A1 - Maier, Johannes A1 - Huber, Michaela A1 - Katzky, Uwe A1 - Perret, Jerome A1 - Wittenberg, Thomas A1 - Palm, Christoph T1 - Force-Feedback-assisted Bone Drilling Simulation Based on CT Data T2 - Bildverarbeitung für die Medizin 2018; Algorithmen - Systeme - Anwendungen; Proceedings des Workshops vom 11. bis 13. März 2018 in Erlangen N2 - In order to fix a fracture using minimally invasive surgery approaches, surgeons are drilling complex and tiny bones with a 2 dimensional X-ray as single imaging modality in the operating room. Our novel haptic force-feedback and visual assisted training system will potentially help hand surgeons to learn the drilling procedure in a realistic visual environment. Within the simulation, the collision detection as well as the interaction between virtual drill, bone voxels and surfaces are important. In this work, the chai3d collision detection and force calculation algorithms are combined with a physics engine to simulate the bone drilling process. The chosen Bullet-Physics-Engine provides a stable simulation of rigid bodies, if the collision model of the drill and the tool holder is generated as a compound shape. Three haptic points are added to the K-wire tip for removing single voxels from the bone. For the drilling process three modes are proposed to emulate the different phases of drilling in restricting the movement of a haptic device. KW - Handchirurgie KW - Osteosynthese KW - Simulation KW - Lernprogramm Y1 - 2018 U6 - https://doi.org/10.1007/978-3-662-56537-7_78 SP - 291 EP - 296 PB - Springer CY - Berlin ER - TY - CHAP A1 - Palm, Christoph A1 - Pelkmann, Annegret A1 - Lehmann, Thomas M. A1 - Spitzer, Klaus T1 - Distortion Correction of Laryngoscopic Images T2 - Advances in quantitative laryngoscopy, voice and speech research, Proceedings of the 3rd international workshop Aachen, RWTH N2 - Laryngoscopic images of the vocal tract are used for diagnostic purposes. Quantitative mea-surements like changes of the glottis size or the surface of the vocal cords during an image sequence can be helpful to describe the healing process or to compare the findings of diffe-rent patients. Typically the endoscopic images are circulary symmetric distorted (barrel di-stortion). Therefore measurements of geometric dimensions depend on the object´s position in the image. In this paper an algorithm is presented which allows the computation of the translational invariant "real" object size by correcting the image distortion without using additional calibration of the optical environment. KW - image distortion KW - camera calibration KW - multiple regression analysis Y1 - 1998 UR - https://pdfs.semanticscholar.org/e9d8/eb27af24bd79f482821441c2bf0eee7b3fe6.pdf?_ga=2.183754286.985176231.1591560247-1467258391.1581026068 SP - 117 EP - 125 ER - TY - CHAP A1 - Palm, Christoph A1 - Vieten, Andrea A1 - Bauer, Dagmar A1 - Pietrzyk, Uwe T1 - Evaluierung von Registrierungsstrategien zur multimodalen 3D-Rekonstruktion von Rattenhirnschnitten T2 - Bildverarbeitung für die Medizin 2006 N2 - In dieser Arbeit werden drei Strategien zur 3D Stapelung von multimodalen Schnittbildern vorgestellt. Die Strategien werden experimentell anhand von Dualtracer-Autoradiographien evaluiert. Dazu werden neue Maße zur Beschreibung der Konsistenz innerhalb einer Modalität und der Konsistenz der Modalitäten untereinander entwickelt, die auf bekannten Registrierungsmetriken basieren. Gerade bezüglich der Konsistenz der Modalitäten untereinander zeigen zwei Strategien die besten Resultate: (1) abwechselnde multimodale Registrierung (2) monomodale Rekonstruktion einer Modalität und multimodale 2D Registrierung der zweiten Modalität. KW - Registrierung KW - Dreidimensionale Rekonstruktion KW - Gehirn KW - Schnittpräparat Y1 - 2006 U6 - https://doi.org/10.1007/3-540-32137-3_51 SP - 251 EP - 255 PB - Springer CY - Berlin ER - TY - GEN A1 - Gräßel, David A1 - Axer, Markus A1 - Palm, Christoph A1 - Dammers, Jürgen A1 - Amunts, Katrin A1 - Pietrzyk, Uwe A1 - Zilles, Karl T1 - Visualization of Fiber Tracts in the Postmortem Human Brain by Means of Polarized Light T2 - NeuroImage KW - Gehirn KW - Bildgebendes Verfahren KW - Polarisiertes Licht KW - Pathologische Anatomie Y1 - 2009 U6 - https://doi.org/10.1016/S1053-8119(09)71415-6 VL - 47 IS - Suppl. 1 SP - 142 ER -