WEB-BASED INTERACTIVE EDITING AND ANALYTICS FOR SUPERVISED SEGMENTATION OF BIOMEDICAL IMAGES A Thesis presented to the Faculty of the Graduate School at the University of Missouri-Columbia In Partial Fulfillment of the Requirements of the Degree Master of Science by RAHUL KUMAR SINGH Dr. Kannappan Palaniappan, Thesis Supervisor DECEMBER 2014 © Copyright by Rahul Kumar Singh 2014 All Rights Reserved The undersigned, appointed by the Dean of the Graduate School, have examined the thesis entitled: WEB-BASED INTERACTIVE EDITING AND ANALYTICS FOR SUPERVISED SEGMENTATION OF BIOMEDICAL IMAGES Presented by Rahul Kumar Singh, a candidate for the degree of Master of Science, and hereby certify that, in their opinion, it is worthy of acceptance. Dr. Kannappan Palaniappan Dr. Jianlin Cheng Dr. Filiz Bunyak ACKNOWLEDGMENTS I would like to thank my advisor Dr. Kannappan Palaniappan for his support and guidance during this project. I completely utilized every opportunity I had during my study at University of Missouri, Columbia with his help and encouragement. I would also like to thank Dr. Stefan Jaeger and Dr. Sema Candemir at the National Institute of Health, Dr. Surya Prasath and Rengarajan Pelapur at the Computation Imaging and Visual Analysis Lab and all my other colleagues for their continuous assistance and advice on this project. I would like to thank Dr. Jianlin Cheng and Dr. Filiz Bunyak for giving me high-quality knowledge and taking out the time to serve on my project committee. I would also like to thank my parents, brother and sister in law for constantly motivating me during this project and guiding me in the right path in all aspects of life and my new born nephew for bringing immense joy in my life. Finally, I thank all my friends, especially Mansha without whose support at the right moment, this wouldn’t have been possible. ii TABLE OF CONTENTS ACKNOWLEDGMENTS ...................................................................................................... ii LIST OF TABLES ................................................................................................................. vi LIST OF FIGURES ............................................................................................................... vi ABSTRACT ........................................................................................................................... xii Chapter 1 Introduction........................................................................................................... 1 1.1 Brief Introduction ........................................................................................................... 1 1.2 FireFly Version 3.0 ........................................................................................................ 2 1.3 FireFly Datasets.............................................................................................................. 5 1.4 Other Similar Tools ...................................................................................................... 10 Chapter 2 FireFly Architecture and Technologies ............................................................ 21 2.1 New System Architecture............................................................................................. 21 2.2 Technologies Used ....................................................................................................... 22 2.3 Local Cache and Screen Buffer .................................................................................... 27 Chapter 3 Multiuser Annotations for Large Image Collections ....................................... 29 3.1 Restructuring of Database ............................................................................................ 29 3.2 Video Sequence vs Image Collection........................................................................... 33 Chapter 4 Segments and Contours Editing ........................................................................ 37 4.1 Need for Segments and Contours Editing .................................................................... 37 iii 4.2 Adding Vertex in Contours and Segments ................................................................... 40 4.3 Deleting Vertex in Contours and Segments ................................................................. 42 4.4 Splitting of Contours and Segments ............................................................................. 44 4.5 Merging of Contours and Segments ............................................................................. 48 4.6 Cases Involving Multiple Edit Operations ................................................................... 56 4.7 Protection and Editing Mode........................................................................................ 60 Chapter 5 Web-based Supervised Image Segmentation ................................................... 61 5.1 MATLAB Interfacing .................................................................................................. 61 5.2 Segmentation Results ................................................................................................... 66 5.3 Alpha Blending of Images............................................................................................ 67 5.4 Loading of Data through PHP Controllers ................................................................... 69 Chapter 6 Data Analytics and Visualization ...................................................................... 71 6.1 Study of Toolkits and Online kits ................................................................................ 72 6.2 Data Visualization in Flex 3 ......................................................................................... 75 6.3 Data Visualization in FireFly ....................................................................................... 77 Chapter 7 Optimizing Web-Based Performance ............................................................... 82 7.1 Dataset Locks ............................................................................................................... 82 7.2 Internet Explorer vs. Other Browsers ........................................................................... 83 7.3 User Interface Improvements for Biomedical Image Annotation ................................ 84 7.4 Incremental Save vs. Bulk Save ................................................................................... 87 iv Chapter 8 New Intuitive GUI Tools .................................................................................... 90 8.1 Creeping of Polygons and Polylines ............................................................................ 91 8.2 Additional Annotation Objects .................................................................................... 94 8.3 Redesign of Save/Display Panel .................................................................................. 99 8.4 Redesign of Frame Advance Panel ............................................................................ 101 8.5 Redesigning of Tools Panel........................................................................................ 101 Chapter 9 Import/Export for Image Analysis .................................................................. 103 9.1 KW 18 Format ............................................................................................................ 103 9.2 Lung Boundaries Format ............................................................................................ 105 9.3 Microvasculature File Format .................................................................................... 106 9.4 Data Analytics File Format for Microvasculature...................................................... 107 9.5 Region of Interest (ROI) Format ................................................................................ 109 9.6 Downloading Results ................................................................................................. 111 Chapter 10 Conclusion & Future Work ........................................................................... 112 10.1 Summary .................................................................................................................... 112 10.2 Future Work ............................................................................................................... 113 Appendix A Development and Debugging in FireFly ...................................................... 118 Appendix B FireFly Manual .............................................................................................. 121 Bibliography ........................................................................................................................ 133 v LIST OF TABLES Table Page 1.1 List of datasets supported by FireFly ................................................................................ 9 2.1 Pros and cons for (a) Silverlight (b) HTML5 (c) Flex [7] .............................................. 23 5.1 Comparison of different technologies [28] ..................................................................... 63 6.1 Flex data visualization table [18] .................................................................................... 76 7.1 FireFly vs. Internet Explorer ........................................................................................... 83 9.1 Details of KW18 format................................................................................................ 105