Visualization Of Tree Research Articles

Utility of Positron Emission Tomography/Computed Tomography in the Detection of Malignancy Within a Choledochal Cyst

A 36-year-old woman with a history of a Todani type IV choledochal cyst (CC), for which she had previously undergone a cystoduodenostomy when she was 13 years old, was admitted and treated for cholangitis. Laboratory investigations revealed a total bilirubin of 31 μmol/L, serum alkaline phosphatase of 70 IU/L, white cell count of 14.08 cells/L, and carbohydrate antigen 19-9 U/mL of 68. Abdomen ultrasonography showed cystic dilatation of the biliary tree. Endoscopic retrograde cholangiopancreatography was unsuccessful. Magnetic resonance cholangiopancreatography (MRCP) showed multiple biliary strictures with ductal dilatation and ductal stones. It also revealed cystic dilatation in the common bile duct, with a maximum diameter of 2.1 cm and filling defect distally (Figure A). Percutaneous transhepatic cholangiography (PTC) was performed, which showed filling defects within the cystoduodenostomy suspicious of malignancy (Figure B). Fusion positron emission tomography/computed tomography (PET/CT) subsequently performed by using 8.2 mCi of [18F-fluorodeoxyglucose] administered intravenously confirmed a metabolically active focus within the cystoduodenostomy corresponding to the location of the filling defect seen at PTC, with a standardized uptake value of 4.6 suggestive of malignancy (Figure C). At surgery, a tumor was found within the 3 × 2.5 × 2 cm CC. En-bloc resection of the CC and cystoduodenostomy including pancreaticoduodenectomy with reconstruction via a double-duct hepaticojejunostomy was performed, and the patient recovered well. Final pathologic examination confirmed a moderately differentiated adenocarcinoma arising within the previous cystoduodenostomy and invading into the muscular wall of the duodenum (Figure D). The diagnosis of a CC often involves multiple imaging modalities.1Corvera C.U. Blumgart L.H. Akhurst T. et al.18F-fluorodeoxyglucose positron emission tomography influences management decisions in patients with biliary cancer.J Am Coll Surg. 2008; 206 (Epub 2007 Oct 1): 57-65Abstract Full Text Full Text PDF PubMed Scopus (197) Google Scholar, 2Park D.H. Kim M.H. Lee S.K. et al.Can MRCP replace the diagnostic role of ERCP for patients with choledochal cysts?.Gastrointest Endosc. 2005; 62: 360-366Abstract Full Text Full Text PDF PubMed Scopus (93) Google Scholar Presently, MRCP might be considered the diagnostic modality of choice because it is noninvasive and demonstrates excellent visualization of the biliary tree.2Park D.H. Kim M.H. Lee S.K. et al.Can MRCP replace the diagnostic role of ERCP for patients with choledochal cysts?.Gastrointest Endosc. 2005; 62: 360-366Abstract Full Text Full Text PDF PubMed Scopus (93) Google Scholar Although previously cystoenterostomy without resection was a popular operation for CC, this is no longer recommended because of the risk of carcinoma developing within the cyst wall, as illustrated by this case. Presently, the management of choice of a CC is complete excision of the entire cyst including all at-risk mucosa to prevent malignant transformation within the remnant wall. Preoperative imaging for cholangiocarcinoma is imperative in assessing the resectability of the tumor, because most patients present late with locally or systemically advanced disease. Several studies have demonstrated the utility of PET/CT in the diagnosis and staging of cholangiocarcinomas that are not diagnosed on standard imaging.3Anderson C.D. Rice M.H. Pinson C.W. et al.Fluorodeoxyglucose PET imaging in the evaluation of gallbladder carcinoma and cholangiocarcinoma.J Gastrointest Surg. 2004; 8: 90-97Crossref PubMed Scopus (288) Google Scholar However, to date, none has reported the use of PET/CT in the detection of malignancy within CCs. The present case is unique because it demonstrates the use of PET/CT in the diagnosis of cholangiocarcinoma arising within a CC. Accurate preoperative diagnosis was important in our patient so that surgical resection with good oncologic clearance was performed. We would like to thank Drs Richard Lo, MBBS, FRCR and Foong-Koon Cheah, MBBS, FRCR from the Department of Radiology, Singapore General Hospital for their assistance in interpreting the radiological images.

How to draw a clustered tree

The visualization of clustered graphs is a classical algorithmic topic that has several practical applications and is attracting increasing research interest. In this paper we deal with the visualization of clustered trees, a problem that is somehow foundational with respect to the one of visualizing a general clustered graph. We show many, in our opinion, surprising results that put in evidence how drawing clustered trees has many sharp differences with respect to drawing “plain” trees. We study a wide class of drawing standards, giving both negative and positive results. Namely, we show that there are clustered trees that do not have any drawing in certain standards and others that require exponential area. On the contrary, for many drawing conventions there are efficient algorithms that allow to draw clustered trees with polynomial asymptotically-optimal area.

Early Identification of Biliary Papillomatosis Through Endoscopic Evaluation of the Common Bile Duct

Purpose: Biliary Papillomatosis is a rare pre-malignant condition which is being increasingly recognized as imaging of the common bile duct improves. Early identification remains important in preventing morbidity and mortality from subsequent cholangicarcinoma. We report the first case of using Spy-Scope (choledochoscopy) in establishing the diagnosis of intraductal biliary papillomatosis. Methods: A 64 year old Asian gentleman presented with RUQ abdominal pain and weight loss of few months duration. There was no fever, chills, nausea or vomiting. Recently, several friends had told him he looked “yellow”. Physical examination revealed an icteric male with right upper quadrant tenderness. Laboratory analysis demonstrated an elevated bilirubin to 3.5 mg/dl, direct 2.5 mg/dl. The AST was elevated to 180 U/L, ALT 220 U/L, alkaline phosphatase 280 U/L and a normal albumin of 3.8 mg/dl. MRI of the abdomen, including MRCP, revealed dilatation of the right hepatic duct and mild intra-hepatic ductal dilation. Cholangiogram showed amorphous filling defects in the right main duct and filling defects in the right intra hepatics. Sphincterotomy was performed. Balloon sweep retrieved friable non-specific debris. To further characterize the filling defects in the biliary tree, a choledochoscope was introduced (Spy Glass, Boston Scientific). On direct visualization, multiple, soft, fleshy, mobile, polypoid growths with fine villous projections on the surface were seen in the intra hepatic ducts. Targeted biopsies were taken from the polypoid tissue using small forceps. Biopsy showed exophytic papillary adenoma and fibro-vascular stroma consistent with Biliary Papillomatosis. Results: Biliary papillomatosis is a rare but increasingly recognized neoplastic disorder of the biliary tree. Common clinical presentations include repeated episodes of abdominal pain, jaundice, acute cholangitis, hemobilia and mucobilia. The disorder typically affects middle aged adults, male to female ratio of 2:1. There is a high malignant potential which progresses via the adenoma-carcinoma sequence. Due to a degree of malignant transformation, surgical resection is necessary. Conclusion: Given the importance of early identification and treatment of this disorder, this novel method as described with endoscopic visualization of the biliary tree (Spy-Scope) should be considered in select patients suspected of having biliary papillomatosis.

Bosque: integrated phylogenetic analysis software

Phylogenetic analyses today involve dealing with computer files in different formats and often several computer programs. Although some widely used applications have integrated important functionalities for such analyses, they still work with local resources only: input/output files (users have to manage them) and local computing (users have sometimes to leave their programs, on their desktop computers, running for extended periods of time). To address these problems we have developed 'Bosque', a multi-platform client-server software that performs standard phylogenetic tasks either locally or remotely on servers, and integrates the results on a local relational database. Bosque performs sequence alignments and graphical visualization and editing of trees, thus providing a powerful environment that integrates all the steps of phylogenetic analyses. http://bosque.udec.cl

EPoS: a modular software framework for phylogenetic analysis

Estimating Phylogenies of Species (EPoS) is a modular software framework for phylogenetic analysis, visualization and data management. It provides a plugin-based system that integrates a storage facility, a rich user interface and the ability to easily incorporate new methods, functions and visualizations. EPoS ships with persistent data management, a set of well-known phylogenetic algorithms and a multitude of tree visualization methods and layouts. Implemented algorithms cover distance-based tree construction, consensus trees and various graph-based supertree methods. The rendering system can be customized for, say, different edge and node styles.

Contrast-enhanced MR cholangiography with Gd-EOB-DTPA in patients with liver cirrhosis: visualization of the biliary ducts in comparison with patients with normal liver parenchyma

The purpose of this study was to assess the quality of biliary duct visualization using Gd-EOB-DTPA-enhanced magnetic resonance cholangiography (EOB-MRC) in patients with liver cirrhosis. Forty adult patients with liver cirrhosis (cirrhosis group) and 20 adult individuals with normal liver parenchyma (control group) underwent EOB-MRC using T1-weighted GRE imaging up to 180 min after Gd-EOB-DTPA administration. Two observers assessed the visualization of each biliary structure and the overall anatomical visualization of the biliary tree. Child-Pugh, MELD score and laboratory findings were compared. The grade of visualization for each evaluated biliary structure was statistically different in the two groups (P = 0.004 to <0.001). The overall EOB-MRC quality was rated as sufficient for anatomical visualization of the biliary tree in all individuals of the control group 20 min after Gd-EOB-DTPA application, but in only 16/40 patients (40%) of the cirrhosis group within 30 min after application. Analysis of the ROC curves revealed that the cut-off values, for non-sufficient visualization of the biliary tree 20 min after Gd-EOB-DTPA application, were MELD scores > or =11 and total serum bilirubin levels > or =30 micromol/l. Consecutively, EOB-MRC in patients with liver cirrhosis resulted in a decreased or even non-visualization of the biliary tree in a substantial percentage of patients.

Stellenwert der kardiovaskulären Magnetresonanztomographie in der Diagnostik der koronaren Herzerkrankung

Currently, the main focus of non-invasive cardiovascular magnetic resonance imaging for diagnosis of coronary artery disease is twofold: first, functional imaging with assessment of the hemodynamic consequences of obstructive coronary artery disease and second, anatomical imaging with direct visualization of the coronary arterial tree. This manuscript will provide an overview of the cardiovascular magnetic resonance imaging modules used to detect coronary artery disease and will update the reader on its current clinical indications with a special focus on functional versus anatomical imaging.

Diagnostic approaches for cholangiocarcinoma

Cholangiocarcinomas arise from the epithelial cells of the bile ducts and are associated with poor prognosis. Despite new diagnostic approaches, the definite diagnosis of this malignancy continues to be challenging. Cholangiocarcinomas often grow longitudinally along the bile duct rather than in a radial direction. Thus, large tumor masses are frequently absent and imaging techniques, including ultrasound, CT, and MRI have only limited sensitivity. Tissue collection during endoscopic (ERCP) and/or percutaneous transhepatic (PTC) procedures are usually used to confirm a definitive diagnosis of cholangiocarcinoma. However, forceps biopsy and brush cytology provide positive results for malignancy in about only 50% of patients. Percutaneous and peroral cholangioscopy using fiber-optic techniques were therefore developed for direct visualization of the biliary tree, yielding additional information about endoscopic appearance and tumor extension, as well as a guided biopsy acquistion. Finally, endoscopic ultrasonography (EUS) complements endoscopic and percutaneous approaches and may provide a tissue diagnosis of tumors in the biliary region through fine-needle aspiration. In the future, new techniques allowing for early detection, including molecular markers, should be developed to improve the diagnostic sensitivity in this increasing tumor entity.

Dendroscope: An interactive viewer for large phylogenetic trees

BackgroundResearch in evolution requires software for visualizing and editing phylogenetic trees, for increasingly very large datasets, such as arise in expression analysis or metagenomics, for example. It would be desirable to have a program that provides these services in an effcient and user-friendly way, and that can be easily installed and run on all major operating systems. Although a large number of tree visualization tools are freely available, some as a part of more comprehensive analysis packages, all have drawbacks in one or more domains. They either lack some of the standard tree visualization techniques or basic graphics and editing features, or they are restricted to small trees containing only tens of thousands of taxa. Moreover, many programs are diffcult to install or are not available for all common operating systems.ResultsWe have developed a new program, Dendroscope, for the interactive visualization and navigation of phylogenetic trees. The program provides all standard tree visualizations and is optimized to run interactively on trees containing hundreds of thousands of taxa. The program provides tree editing and graphics export capabilities. To support the inspection of large trees, Dendroscope offers a magnification tool. The software is written in Java 1.4 and installers are provided for Linux/Unix, MacOS X and Windows XP.ConclusionDendroscope is a user-friendly program for visualizing and navigating phylogenetic trees, for both small and large datasets.

TreeViewJ: An application for viewing and analyzing phylogenetic trees

BackgroundPhylogenetic trees are widely used to visualize evolutionary relationships between different organisms or samples of the same organism. There exists a variety of both free and commercial tree visualization software available, but limitations in these programs often require researchers to use multiple programs for analysis, annotation, and the production of publication-ready images.ResultsWe present TreeViewJ, a Java tool for visualizing, editing and analyzing phylogenetic trees. The software allows researchers to color and change the width of branches that they wish to highlight, and add names to nodes. If collection dates are available for taxa, the software can map them onto a timeline, and sort the tree in ascending or descending date order.ConclusionTreeViewJ is a tool for researchers to visualize, edit, "decorate," and produce publication-ready images of phylogenetic trees. It is open-source, and released under an GPL license, and available at .

A Single Institutionʼs Initial Experience with Spyglass™ in the Diagnosis and Management of Biliary Disease during ERCP

Purpose: To evaluate the clinical utility, safety and ease of use of SpyGlass™ (a single-operator peroral cholangiopancreatoscopy system) during endoscopic retrograde cholangiopancreotography (ERCP). Methods: A retrospective chart review was performed of the ERCP cases during which Spyglass™ was used. For each case, the following outcomes were assessed: success of introducing the device into the bile duct; successful identification of filling defects; use and success of electrohydraulic lithotripsy (if performed); use and success of directly visualized forceps biopsies; and yield of biopsies. Results: Spyglass™ cholangiopancreatoscopy was attempted in 6 patients. A single operator performed each case. Indications for Spyglass™ included: unexplained abdominal pain of suspected biliary origin (N = 1) and filling defects seen on initial cholangiogram [suspected choledocolithiasias (N = 3) and malignant stricture (N = 2)]. Cannulation with Spyglass™ was successful in 5 of 6 patients (83.3%). The single failed cannulation was due to difficult anatomy from a suspected malignant biliary stricture in the distal common bile duct. Identification of filling defects was achieved in 4 of the 5 successful cannulations (3 with stones, 1 with malignancy). Biopsies were performed in 1 case with a successful diagnosis of a ductal carcinoma. Therapy using electrohydraulic lithotripsy (EHL) via the Spyglass™ device was attempted in 2 patients (1 with a common bile duct stone, 1 with a cystic duct stone). Partial clearance was achieved in each case. Failure of successful lithotripsy was due to (1) the size of the common bile duct stone and (2) inability to maintain good stone to EHL probe contact in the cystic duct. No procedure related complications occurred. Conclusion: In this small retrospective review, the Spyglass system demonstrated adequate visualization of the biliary tree to facilitate the diagnosis of biliary strictures and lithotripsy of large CBD stones during ERCP. Further investigation to identify the optimum patient characteristics for cholangiopancreatoscopy with this system is required and ongoing.

System for the analysis and visualization of large 3D anatomical trees

Modern micro-CT and multi-detector helical CT scanners can produce high-resolution 3D digital images of various anatomical trees. The large size and complexity of these trees make it essentially impossible to define them interactively. Automatic approaches have been proposed for a few specific problems, but none of these approaches guarantee extracting geometrically accurate multi-generational tree structures. This paper proposes an interactive system for defining and visualizing large anatomical trees and for subsequent quantitative data mining. The system consists of a large number of tools for automatic image analysis, semi-automatic and interactive tree editing, and an assortment of visualization tools. Results are presented for a variety of 3D high-resolution images.

Imaging techniques for the vulnerable coronary plaque

The goal of this article is to illustrate the main invasive and noninvasive diagnostic modalities to image the vulnerable coronary plaque, which is responsible for acute coronary syndrome. The main epidemiologic and histological issues are briefly discussed in order to provide an adequate background. Comprehensive coronary atherosclerosis imaging should involve visualization of the entire coronary artery tree and plaque characterization, including three-dimensional morphology, relationship with the lumen, composition, vascular remodelling and presence of inflammation. No single technique provides such a comprehensive description, and no available modality extensively identifies the vulnerable plaque. In particular, we describe multislice computed tomography, which at present seems to be the most promising noninvasive tool for an exhaustive image-based quantification of coronary atherosclerosis.

Three-Dimensional Phylogeny Explorer: Distinguishing paralogs, lateral transfer, and violation of "molecular clock" assumption with 3D visualization

BackgroundConstruction and interpretation of phylogenetic trees has been a major research topic for understanding the evolution of genes. Increases in sequence data and complexity are creating a need for more powerful and insightful tree visualization tools.ResultsWe have developed 3D Phylogeny Explorer (3DPE), a novel phylogeny tree viewer that maps trees onto three spatial axes (species on the X-axis; paralogs on Z; evolutionary distance on Y), enabling one to distinguish at a glance evolutionary features such as speciation; gene duplication and paralog evolution; lateral gene transfer; and violation of the "molecular clock" assumption. Users can input any tree on the online 3DPE, then rotate, scroll, rescale, and explore it interactively as "live" 3D views. All objects in 3DPE are clickable to display subtrees, connectivity path highlighting, sequence alignments, and gene summary views, and etc. To illustrate the value of this visualization approach for microbial genomes, we also generated 3D phylogeny analyses for all clusters from the public COG database. We constructed tree views using well-established methods and graph algorithms. We used Scientific Python to generate VRML2 3D views viewable in any web browser.Conclusion3DPE provides a novel phylogenetic tree projection method into 3D space and its web-based implementation with live 3D features for reconstruction of phylogenetic trees of COG database.

A New Short Cholangioscope for Peroral Cholangioscopy

Background: The mother-baby technique for peroral cholangioscopy permits direct visualization of the biliary tree. Conventional peroral cholangioscopy is performed by introducing a small calibre cholangioscope (C) through the instrumentation channel of the duodenoscope (D). Due to the length of the C (> 180 cm) its handling is cumbersome, torque transmission is reduced and angulation in the biliary tract is limited. Instrumenation options via the C are restricted because of its small instrumentation channel (12 mm).

The formation of a tree leaf

In this article, we build a mathematical model to understand the formation of a tree leaf. Our model is based on the idea that a leaf tends to maximize internal efficiency by developing an efficient transport system for transporting water and nutrients. The meaning of “the efficient transport system” may vary as the type of the tree leave varies. In this article, we will demonstrate that tree leaves have different shapes and venation patterns mainly because they have adopted different efficient transport systems. The efficient transport system of a tree leaf built here is a modified version of the optimal transport path, which was introduced by the author in [Comm. Cont. Math. 5 (2003) 251–279; Calc. Var. Partial Differ. Equ. 20 (2004) 283–299; Boundary regularity of optimal transport paths, Preprint] to study the phenomenon of ramifying structures in mass transportation. In the present paper, the cost functional on transport systems is controlled by two meaningful parameters. The first parameter describes the economy of scale which comes with transporting large quantities together, while the second parameter discourages the direction of outgoing veins at each node from differing much from the direction of the incoming vein. Under the same initial condition, efficient transport systems modeled by different parameters will provide tree leaves with different shapes and different venation patterns. Based on this model, we also provide some computer visualization of tree leaves, which resemble many known leaves including the maple and mulberry leaf. It demonstrates that optimal transportation plays a key role in the formation of tree leaves.

A Novel Method for Visualization of Entire Coronary Arterial Tree

The complexity of the coronary circulation especially in the deep layers largely evades experimental investigations. Hence, virtual/computational models depicting structure-function relation of the entire coronary vasculature including the deep layer are imperative. In order to interpret such anatomically based models, fast and efficient visualization algorithms are essential. The complexity of such models, which include vessels from the large proximal coronary arteries and veins down to the capillary level (3 orders of magnitude difference in diameter), is a challenging visualization problem since the resulting geometrical representation consists of millions of vessel segments. In this study, a novel method for rendering the entire porcine coronary arterial tree down to the first segments of capillaries interactively is described which employs geometry reduction and occlusion culling techniques. Due to the tree-shaped nature of the vasculature, these techniques exploit the geometrical topology of the object to achieve a faster rendering speed while still handling the full complexity of the data. We found a significant increase in performance combined with a more accurate, gap-less representation of the vessel segments resulting in a more interactive visualization and analysis tool for the entire coronary arterial tree. The proposed techniques can also be applied to similar data structures, such as neuronal trees, airway structures, bile ducts, and other tree-like structures. The utility and future applications of the proposed algorithms are explored.

Binary Partition Tree for Semantic Object Extraction and Image Segmentation

In this work, we demonstrate a systematic way to analyze a binary partition tree representation of natural images for the purposes of archiving and segmentation. Within the tree structure, these problems are transformed into locating prevalent tree branches. With a user interface these points can be found manually by browsing branches. However, tree visualization is difficult due to the high node density. A simpler version of the tree is desired which facilitates subsequent retrieval whilst maintaining as much semantic detail as possible. By studying the evolution of region statistics, our method highlights nodes which represent the boundary between salient detail and provide a set of tree levels from which simplifications and segmentations can be derived. A series of subjective tests are performed to demonstrate the effectiveness of using the simplified trees for object extraction. Segmentation results are compared to ground truths showing semantic content is maintained

Constructing program animations using a pattern based approach

The aim of this paper is to discuss how our pattern-based strategy for the visualization of data and control flow can effectively be used to animate the program and exhibit its behavior. That result allows us to propose its use for Program Comprehension. The animator uses well known compiler techniques to inspect the source code in order to extract the necessary information to visualize it and understand program execution. We convert the source program into an internal decorated (or attributed) abstract syntax tree and then we visualize the structure by traversing it, and applying visualization rules at each node according to a pre-defined rule-base. In order to calculate the next step in the program execution, a set of rewriting rules are applied to the tree. The visualization of this new tree is shown and the program animation is constructed using an iterative process. No changes are made in the source code, and the execution is simulated step by step. Several examples of visualization are shown to illustrate the approach and support our idea of applying it in the context of a Program Comprehension environment.

TreeDyn: towards dynamic graphics and annotations for analyses of trees

BackgroundAnalyses of biomolecules for biodiversity, phylogeny or structure/function studies often use graphical tree representations. Many powerful tree editors are now available, but existing tree visualization tools make little use of meta-information related to the entities under study such as taxonomic descriptions or gene functions that can hardly be encoded within the tree itself (if using popular tree formats). Consequently, a tedious manual analysis and post-processing of the tree graphics are required if one needs to use external information for displaying or investigating trees.ResultsWe have developed TreeDyn, a tool using annotations and dynamic graphical methods for editing and analyzing multiple trees. The main features of TreeDyn are 1) the management of multiple windows and multiple trees per window, 2) the export of graphics to several standard file formats with or without HTML encapsulation and a new format called TGF, which enables saving and restoring graphical analysis, 3) the projection of texts or symbols facing leaf labels or linked to nodes, through manual pasting or by using annotation files, 4) the highlight of graphical elements after querying leaf labels (or annotations) or by selection of graphical elements and information extraction, 5) the highlight of targeted trees according to a source tree browsed by the user, 6) powerful scripts for automating repetitive graphical tasks, 7) a command line interpreter enabling the use of TreeDyn through CGI scripts for online building of trees, 8) the inclusion of a library of packages dedicated to specific research fields involving trees.ConclusionTreeDyn is a tree visualization and annotation tool which includes tools for tree manipulation and annotation and uses meta-information through dynamic graphical operators or scripting to help analyses and annotations of single trees or tree collections.