RT-GAN: Recurrent Temporal GAN for Adding Lightweight Temporal Consistency to Frame-Based Domain Translation Approaches

While developing new unsupervised domain translation methods for endoscopy videos, it is typical to start with approaches that initially work for individual frames without temporal consistency. Once an individual-frame model has been finalized, additional contiguous frames are added with a modified deep learning architecture to train a new model for temporal consistency. This transition to temporally-consistent deep learning models, however, requires significantly more computational and memory resources for training. In this paper, we present a lightweight solution with a tunable temporal parameter, RT-GAN (Recurrent Temporal GAN), for adding temporal consistency to individual frame-based approaches that reduces training requirements by a factor of 5. We demonstrate the effectiveness of our approach on two challenging use cases in colonoscopy: haustral fold segmentation (indicative of missed surface) and realistic colonoscopy simulator video generation. The datasets, accompanying code, and pretrained models will be made available at \url{https://github.com/nadeemlab/CEP}.

CLTS-GAN: Color-Lighting-Texture-Specular Reflection Augmentation for Colonoscopy

Automated analysis of optical colonoscopy (OC) video frames (to assist endoscopists during OC) is challenging due to variations in color, lighting, texture, and specular reflections. Previous methods either remove some of these variations via preprocessing (making pipelines cumbersome) or add diverse training data with annotations (but expensive and time-consuming). We present CLTS-GAN, a new deep learning model that gives fine control over color, lighting, texture, and specular reflection synthesis for OC video frames. We show that adding these colonoscopy-specific augmentations to the training data can improve state-of-the-art polyp detection/segmentation methods as well as drive next generation of OC simulators for training medical students. The code and pre-trained models for CLTS-GAN are available on Computational Endoscopy Platform GitHub (https://github.com/nadeemlab/CEP).

FoldIt: Haustral Folds Detection and Segmentation in Colonoscopy Videos

Haustral folds are colon wall protrusions implicated for high polyp miss rate during optical colonoscopy procedures. If segmented accurately, haustral folds can allow for better estimation of missed surface and can also serve as valuable landmarks for registering pre-treatment virtual (CT) and optical colonoscopies, to guide navigation towards the anomalies found in pre-treatment scans. We present a novel generative adversarial network, FoldIt, for feature-consistent image translation of optical colonoscopy videos to virtual colonoscopy renderings with haustral fold overlays. A new transitive loss is introduced in order to leverage ground truth information between haustral fold annotations and virtual colonoscopy renderings. We demonstrate the effectiveness of our model on real challenging optical colonoscopy videos as well as on textured virtual colonoscopy videos with clinician-verified haustral fold annotations. All code and scripts to reproduce the experiments of this paper will be made available via our Computational Endoscopy Platform at https://github.com/nadeemlab/CEP.

Visualizing Missing Surfaces In Colonoscopy Videos using Shared Latent Space Representations

Optical colonoscopy (OC), the most prevalent colon cancer screening tool, has a high miss rate due to a number of factors, including the geometry of the colon (haustral fold and sharp bends occlusions), endoscopist inexperience or fatigue, endoscope field of view, etc. We present a framework to visualize the missed regions per-frame during the colonoscopy, and provides a workable clinical solution. Specifically, we make use of 3D reconstructed virtual colonoscopy (VC) data and the insight that VC and OC share the same underlying geometry but differ in color, texture and specular reflections, embedded in the OC domain. A lossy unpaired image-to-image translation model is introduced with enforced shared latent space for OC and VC. This shared latent space captures the geometric information while deferring the color, texture, and specular information creation to additional Gaussian noise input. This additional noise input can be utilized to generate one-to-many mappings from VC to OC and OC to OC.

Augmenting Colonoscopy using Extended and Directional CycleGAN for Lossy Image Translation

Colorectal cancer screening modalities, such as optical colonoscopy (OC) and virtual colonoscopy (VC), are critical for diagnosing and ultimately removing polyps (precursors of colon cancer). The non-invasive VC is normally used to inspect a 3D reconstructed colon (from CT scans) for polyps and if found, the OC procedure is performed to physically traverse the colon via endoscope and remove these polyps. In this paper, we present a deep learning framework, Extended and Directional CycleGAN, for lossy unpaired image-to-image translation between OC and VC to augment OC video sequences with scale-consistent depth information from VC, and augment VC with patient-specific textures, color and specular highlights from OC (e.g, for realistic polyp synthesis). Both OC and VC contain structural information, but it is obscured in OC by additional patient-specific texture and specular highlights, hence making the translation from OC to VC lossy. The existing CycleGAN approaches do not handle lossy transformations. To address this shortcoming, we introduce an extended cycle consistency loss, which compares the geometric structures from OC in the VC domain. This loss removes the need for the CycleGAN to embed OC information in the VC domain. To handle a stronger removal of the textures and lighting, a Directional Discriminator is introduced to differentiate the direction of translation (by creating paired information for the discriminator), as opposed to the standard CycleGAN which is direction-agnostic. Combining the extended cycle consistency loss and the Directional Discriminator, we show state-of-the-art results on scale-consistent depth inference for phantom, textured VC and for real polyp and normal colon video sequences. We also present results for realistic pendunculated and flat polyp synthesis from bumps introduced in 3D VC models.

LMap: Shape-Preserving Local Mappings for Biomedical Visualization

Visualization of medical organs and biological structures is a challenging task because of their complex geometry and the resultant occlusions. Global spherical and planar mapping techniques simplify the complex geometry and resolve the occlusions to aid in visualization. However, while resolving the occlusions these techniques do not preserve the geometric context, making them less suitable for mission-critical biomedical visualization tasks. In this paper, we present a shape-preserving local mapping technique for resolving occlusions locally while preserving the overall geometric context. More specifically, we present a novel visualization algorithm, LMap, for conformally parameterizing and deforming a selected local region-of-interest (ROI) on an arbitrary surface. The resultant shape-preserving local mappings help to visualize complex surfaces while preserving the overall geometric context. The algorithm is based on the robust and efficient extrinsic Ricci flow technique, and uses the dynamic Ricci flow algorithm to guarantee the existence of a local map for a selected ROI on an arbitrary surface. We show the effectiveness and efficacy of our method in three challenging use cases: (1) multimodal brain visualization, (2) optimal coverage of virtual colonoscopy centerline flythrough, and (3) molecular surface visualization.

C2A: Crowd Consensus Analytics for Virtual Colonoscopy

We present a medical crowdsourcing visual analytics platform called C{$^2$}A to visualize, classify and filter crowdsourced clinical data. More specifically, C$^2$A is used to build consensus on a clinical diagnosis by visualizing crowd responses and filtering out anomalous activity. Crowdsourcing medical applications have recently shown promise where the non-expert users (the crowd) were able to achieve accuracy similar to the medical experts. This has the potential to reduce interpretation/reading time and possibly improve accuracy by building a consensus on the findings beforehand and letting the medical experts make the final diagnosis. In this paper, we focus on a virtual colonoscopy (VC) application with the clinical technicians as our target users, and the radiologists acting as consultants and classifying segments as benign or malignant. In particular, C$^2$A is used to analyze and explore crowd responses on video segments, created from fly-throughs in the virtual colon. C$^2$A provides several interactive visualization components to build crowd consensus on video segments, to detect anomalies in the crowd data and in the VC video segments, and finally, to improve the non-expert user's work quality and performance by A/B testing for the optimal crowdsourcing platform and application-specific parameters. Case studies and domain experts feedback demonstrate the effectiveness of our framework in improving workers' output quality, the potential to reduce the radiologists' interpretation time, and hence, the potential to improve the traditional clinical workflow by marking the majority of the video segments as benign based on the crowd consensus.

Visualization Framework for Colonoscopy Videos

We present a visualization framework for annotating and comparing colonoscopy videos, where these annotations can then be used for semi-automatic report generation at the end of the procedure. Currently, there are approximately 14 million colonoscopies performed every year in the US. In this work, we create a visualization tool to deal with the deluge of colonoscopy videos in a more effective way. We present an interactive visualization framework for the annotation and tagging of colonoscopy videos in an easy and intuitive way. These annotations and tags can later be used for report generation for electronic medical records and for comparison at an individual as well as group level. We also present important use cases and medical expert feedback for our visualization framework.

Corresponding Supine and Prone Colon Visualization Using Eigenfunction Analysis and Fold Modeling

We present a method for registration and visualization of corresponding supine and prone virtual colonoscopy scans based on eigenfunction analysis and fold modeling. In virtual colonoscopy, CT scans are acquired with the patient in two positions, and their registration is desirable so that physicians can corroborate findings between scans. Our algorithm performs this registration efficiently through the use of Fiedler vector representation (the second eigenfunction of the Laplace-Beltrami operator). This representation is employed to first perform global registration of the two colon positions. The registration is then locally refined using the haustral folds, which are automatically segmented using the 3D level sets of the Fiedler vector. The use of Fiedler vectors and the segmented folds presents a precise way of visualizing corresponding regions across datasets and visual modalities. We present multiple methods of visualizing the results, including 2D flattened rendering and the corresponding 3D endoluminal views. The precise fold modeling is used to automatically find a suitable cut for the 2D flattening, which provides a less distorted visualization. Our approach is robust, and we demonstrate its efficiency and efficacy by showing matched views on both the 2D flattened colons and in the 3D endoluminal view. We analytically evaluate the results by measuring the distance between features on the registered colons, and we also assess our fold segmentation against 20 manually labeled datasets. We have compared our results analytically to previous methods, and have found our method to achieve superior results. We also prove the hot spots conjecture for modeling cylindrical topology using Fiedler vector representation, which allows our approach to be used for general cylindrical geometry modeling and feature extraction.

Radiative Transport Based Flame Volume Reconstruction from Videos

We introduce a novel approach for flame volume reconstruction from videos using inexpensive charge-coupled device (CCD) consumer cameras. The approach includes an economical data capture technique using inexpensive CCD cameras. Leveraging the smear feature of the CCD chip, we present a technique for synchronizing CCD cameras while capturing flame videos from different views. Our reconstruction is based on the radiative transport equation which enables complex phenomena such as emission, extinction, and scattering to be used in the rendering process. Both the color intensity and temperature reconstructions are implemented using the CUDA parallel computing framework, which provides real-time performance and allows visualization of reconstruction results after every iteration. We present the results of our approach using real captured data and physically-based simulated data. Finally, we also compare our approach against the other state-of-the-art flame volume reconstruction methods and demonstrate the efficacy and efficiency of our approach in four different applications: (1) rendering of reconstructed flames in virtual environments, (2) rendering of reconstructed flames in augmented reality, (3) flame stylization, and (4) reconstruction of other semitransparent phenomena.