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Referenzfreie Dreidimensionale Rekonstruktion von Digitalisierten Histologischen Schnittserien
No full textAlthough first 3-D reconstructions of minute structures were made over 130 years
ago, the need to understand the shape and morphology of various specimens at the
microscopic level has increased significantly in the last decade. Since volumetric
imaging techniques like computed tomography or magnetic resonance imaging are
still limited regarding spatial resolution and availability, an interest in the digital
reconstruction of histological tissue preparations prepared and stained according to
the scientific question has evolved.
One fundamental technique in 3D histology reconstruction is the use of image
registration for alignment of slice images and reversal of slice deformations. Here,
the individual registration components are often chosen to best fit the data at hand.
This thesis uses a rigid transformation model for simple alignment and a non-rigid,
non-parametric image transform for image unwarping. The core principle of the unwarping
strategy is the iterative Gauss-Seidel method, which is capable of selectively
eliminating higher frequency errors from given functions consisting of superimposed
signals of different wavelengths. Evaluation strategies like the Sum of Squared Distances,
Target Registration Error and Graylevel Cooccurrence Matrices are ways to
assess the quality of match between slices and the coherence of reconstructed histology
volumes.
The histological preparation procedure steps like resection, embedding, cutting
and staining significantly destroy the tissue, and the digitization step leads to disambiguities
and information loss regarding the shape of structures. The image data
sets are therefore inherently afflicted with a large number of artifacts like intensity
variances, foldings, deformations or missing parts.
The preprocessing and reconstruction pipeline starts with the gray value conversion
of color images to reduce the computational effort. As one of the two main
contributions of the work a novel intensity standardization for histological image
sequences is proposed. Here, percentile values of individual slice histograms are determined,
and corresponding percentile values treated as list of function values. The
Gauss-Seidel method is used to eliminate the higher frequency intensity variances,
but preserve the lower frequency differences stemming from changing tissue content.
For an entire slice data set, a mean intensity correction of 0.45 and mean standard
deviation of correction of only 5.03 – half of the correction other methods achieved –
demonstrates a moderate adaption of the original intensity values, while qualitative
results show good contrast and smooth appearance. After optional replacement of
defective or missing slice images and possibly manual sorting of the image data set,
a first simple 3D reconstruction is achieved by rigid image registration and stacking.
The remaining nonlinear slice deformations prevent real coherence of the anatomy.
The second main contribution of the work is the adaptation of the Gauss-Seidel
method for image sequences. While the non-rigid image registration process provides
a possibility to emulate the slice deformations and thus to reverse them, the Gauss-
Seidel method determines how these deformations are eliminated by an iterative
update of the individual images, taking into account their local neighborhood. The
method is suitable for large datasets, since it does not require the entire dataset
in memory. Experiments show that the method converges quickly, and experiments
with synthetic data with known deformations suggest that the true deformation of
the slices is effectively reversed, with the Mean Target Registration Error being below
1 pixel offset to the original CT data set after 5 iterations. Visually, the results are
convincing and provide instructive insights into microscopic morphology.
Further improvements of the proposed reconstruction pipeline include a gray level
conversion based on stain protocol or structure-of-interest, better defect slice replacement
methods, or automated methods to restore the correct slice sequence. The intensity
matching method could be adapted based on the tissue content. For large
data sets, the Gauss-Seidel unwarping method should be modified to a multilevel
approach. Possible applications include better anatomical teaching, improvement of
in-vivo 3D imaging protocols or digital pathology.Obwohl die ersten 3-D-Rekonstruktionen von kleinsten Strukturen bereits vor über
130 Jahren vogenommen wurden, hat die Notwendigkeit die Form und Morphologie
verschiedener Präparate auch auf mikroskopischer Ebene zu verstehen im letzten
Jahrzehnt deutlich zugenommen. Da volumetrische bildgebende Verfahren wie Computertomographie
oder Magnetresonanztomographie sowohl bezüglich ihrer räumlichen
Auflösung als auch Verfügbarkeit limitiert sind, hat sich ein Interesse an
der digitalen Rekonstruktion histologischer Gewebepräparate entwickelt, die der wissenschaftlichen
Fragestellung entsprechend präpariert und gefärbt wurden.
Eine grundlegende Technik für die 3-D Histologierekonstruktion ist die Bildregistrierung,
die zur Ausrichtung und zum Entfernen von Schichtdeformationen verwendet
wird. Hierbei werden die individuellen Komponenten der Registrierung meist
den konkret vorliegenden Daten angepasst. Diese Arbeit verwendet ein starres Transformationsmodell
für die einfache Schichtausrichtung, und eine nicht-starre, nichtparametrische
Bildtransformation zur Bildentzerrung. Das Kernprinzip der Entzerrung
ist das iterative Gauss-Seidel-Verfahren, das in der Lage ist bei Funktionen, in
denen Signale verschiedener Wellenlänge überlagert sind, selektiv Fehler höherer Frequenz
zu eliminieren. Auswertestrategien wie die Summe der quadrierten Differenzen,
der Target Registration Error und Maße basierend auf Grauwertmatrizen bewerten
die Ähnlichkeit von Einzelschichten und die Kohärenz rekonstruierter Histologievolumen.
Histologische Präparationsschritte wie Resektion, Einbettung, Schneiden und Färben
zerstören das Gewebe, und die Digitalisierung führt zu Zweideutigkeiten und Informationsverlust
bezüglich der Form einzelner Strukturen. Die Bilddatensätze sind
dadurch inhärent mit einer großen Zahl von Bildartefakten wie Intensitätsvarianzen,
Faltungen, Deformationen, oder fehlenden Teilen behaftet.
Die Vorverarbeitungs- und Rekonstruktionspipeline beginnt mit der Grauwertkonvertierung
der Farbbilder, um den Rechenaufwand zu reduzieren. Als einer der beiden
Hauptbeiträge der Arbeit wird eine neuartige Intensitätsstandardisierung für
histologische Bildsequenzen vorgeschlagen. Hier werden Perzentilwerte der einzelnen
Schichthistogramme bestimmt, und korrespondierende Perzentile als Liste von
Funktionswerten zusammengefasst. Das Gauss-Seidel-Verfahren wird dann verwendet
um hochfrequente Intensitätsänderungen zu eliminieren, während niederfrequente
Änderungen, die sich durch sich ändernde Gewebeanteile ergeben, erhalten werden.
Für einen gesamten Bilddatensatz ergibt sich beispielsweise eine mittlere Intensitätskorrektur
von 0.45 und eine mittlere Standardabweichung der Korrektur von nur
5.03 – was etwa die Hälfte anderer Verfahren ist –, was einer moderaten Anpassung
der Originalintensitäten ist, wobei qualitativ guter Kontrast und ein homogener
Eindruck entsteht. Nach optionaler Ersetzung defekter oder fehlender Schichtbilder
und möglicherweise manueller Sortierung des Bilddatensatzes wird über eine starre
Bildregistrierung eine erste einfache 3D-Rekonstruktion erreicht.
Die verbleibenden nichtlinearen Schichtverformungen verhindern eine wirkliche
Kohärenz der Anatomie. Der zweite Hauptbeitrag der Arbeit ist daher die Übertragung
des bekannten Gauß-Seidel-Verfahrens für die Anwendung auf Bildsequenzen.
Während die nicht-starre Bildregistrierung eine Möglichkeit liefert, die Schichtverformungen
prinzipiell nachzubilden und damit auch rückgängig zu machen, so bestimmt
die Gauß-Seidel-Methode, inwiefern diese Verformungen durch eine iterative Verarbeitung
der Einzelbilder unter Berücksichtigung der Nachbarschaft beseitigt werden.
Das Verfahren ist für große Datensätze geeignet, da es nicht den gesamten Datensatz
im Speicher benötigt. Die Experimente zeigen, dass das Verfahren schnell konvergiert,
und Experimente mit synthetischen Daten mit bekannten Verformungen legen nahe,
dass die wahre Deformation der Schichten rückgängig gemacht wird, mit einem mittleren
Target Registration Error von unter 1 Pixel Abweichung vom Original-CT nach
5 Iterationen. Visuell sind die Ergebnisse überzeugend und bieten lehrreiche Einblicke
in die mikroskopische Morphologie.
Weitere Verbesserungen der vorgestellten Rekonstruktionsprozedur beinhalten eine
Grauwertkonversion basierend auf Färbeprotokoll oder anhand besonders interessanter
Strukturen, bessere Methoden um defekte Schichten oder Teile zu ersetzen,
oder automatisierte Methoden um die korrekte Schichtreihenfolge herzustellen. Die
Methode zur Intensitätsstandardisierung könnte je nach konkretem Gewebeanteil
angepasst werden. Für große Datensätze sollte das Gauss-Seidel-Verfahren auf einen
Multilevelansatz erweitert werden. Mögliche Anwendungen sind verbesserte Anatomieausbildung,
Verbesserung von in-vivo 3D Aufnahmeverfahren oder digitale Pathologie
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
Author Under Sail The Imagination of Jack London, 1893-1902
No full textIn Author Under Sail, Jay Williams offers the first complete literary biography of Jack London as a professional writer engaged in the labor of writing. It examines the authorial imagination in London's work, the use of imagination in both his fiction and nonfiction, and the ways he defined imagination in the creative process in his business dealings with his publishers, editors, and agents. In this first volume of a two-volume biography, Williams traverses the years 1893 to 1902, from London's "Story of a Typhoon" to The People of the Abyss. The Jack London who emerges in the pages of Author Under Sail is a writer whose partnership with publishers, most notably his productive alliance with George Brett of Macmillan, was one of the most formative in American literary history. London pioneered many author models during the heyday of realism and naturalism, blurring the boundaries of these popular genres by focusing on absorption and theatricality and the representation of the seen and unseen. London created an impassioned, sincere, and extremely personal realism unlike that of other American writers of the time. Author Under Sail is a literary tour de force that reveals the full range of London as writer, creative citizen, and entrepreneur at the same time it sheds light on the maverick side of machine-age literature.Intro -- Title Page -- Copyright Page -- Dedication -- Contents -- Acknowledgments -- Introduction -- 1. Spirit Truth -- 2. From Absorption to Theatricality and Back Again -- 3. "I Will Build a New Present" -- 4. Sons as Authors -- 5. Fathers as Publishers -- 6. The Daughter as Author -- 7. Lovers as Authors -- 8. At Sea with the Family -- 9. Yellow News, Yellow Stories -- 10. The Return Home -- Notes -- Bibliography -- Index -- About Jay WilliamsIn Author Under Sail, Jay Williams offers the first complete literary biography of Jack London as a professional writer engaged in the labor of writing. It examines the authorial imagination in London's work, the use of imagination in both his fiction and nonfiction, and the ways he defined imagination in the creative process in his business dealings with his publishers, editors, and agents. In this first volume of a two-volume biography, Williams traverses the years 1893 to 1902, from London's "Story of a Typhoon" to The People of the Abyss. The Jack London who emerges in the pages of Author Under Sail is a writer whose partnership with publishers, most notably his productive alliance with George Brett of Macmillan, was one of the most formative in American literary history. London pioneered many author models during the heyday of realism and naturalism, blurring the boundaries of these popular genres by focusing on absorption and theatricality and the representation of the seen and unseen. London created an impassioned, sincere, and extremely personal realism unlike that of other American writers of the time. Author Under Sail is a literary tour de force that reveals the full range of London as writer, creative citizen, and entrepreneur at the same time it sheds light on the maverick side of machine-age literature.Description based on publisher supplied metadata and other sources.Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, YYYY. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries
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