Colonoscopy 3D Video Dataset with Paired Depth from 2D-3D Registration

Screening colonoscopy is an important clinical application for several 3D computer vision techniques, including depth estimation, surface reconstruction, and missing region detection. However, the development, evaluation, and comparison of these techniques in real colonoscopy videos remain largely qualitative due to the difficulty of acquiring ground truth data. In this work, we present a Colonoscopy 3D Video Dataset (C3VD) acquired with a high definition clinical colonoscope and high-fidelity colon models for benchmarking computer vision methods in colonoscopy. We introduce a novel multimodal 2D-3D registration technique to register optical video sequences with ground truth rendered views of a known 3D model. The different modalities are registered by transforming optical images to depth maps with a Generative Adversarial Network and aligning edge features with an evolutionary optimizer. This registration method achieves an average translation error of 0.321 millimeters and an average rotation error of 0.159 degrees in simulation experiments where error-free ground truth is available. The method also leverages video information, improving registration accuracy by 55.6% for translation and 60.4% for rotation compared to single frame registration. 22 short video sequences were registered to generate 10,015 total frames with paired ground truth depth, surface normals, optical flow, occlusion, six degree-of-freedom pose, coverage maps, and 3D models. The dataset also includes screening videos acquired by a gastroenterologist with paired ground truth pose and 3D surface models. The dataset and registration source code are available at durr.jhu.edu/C3VD

Novel Long Noncoding RNA miR205HG Functions as an Esophageal Tumor-Suppressive Hedgehog Inhibitor

Barrett’s esophagus (BE) is a precursor to esophageal adenocarcinoma (EAC). Recently, long noncoding RNAs (lncRNAs) have been identified as key regulators of biological pathways. However, involvement of lncRNAs in the development of BE and EAC has not been well-studied. The aims of the current study were: (1) to study involvement of the lncRNA, miR205HG, in the development of BE and EAC; (2) to clarify the role of miR205HG in in vitro and in vivo experiments; and (3) to investigate the mechanism of miR205HG involving the Hedgehog (Hh) signaling pathway. These experiments revealed that miR205HG was downregulated in EAC vs. normal esophageal epithelia (NE) as well as in EAC cell lines, and its forced overexpression inhibited EAC cell proliferation and cell cycle progression in vitro. Similarly, overexpression of miR205HG inhibited xenograft tumor growth in mice In vivo. Finally, we show that one mechanism of action of miR205HG involves the Hh signaling pathway: miR205HG and Hh expression levels were inversely correlated in both EAC (r = −0.73) and BE (r = −0.83) tissues, and in vitro studies revealed details of Hh signaling inhibition induced by miR205HG. In conclusion, these findings establish that lncRNA miR205HG functions as a tumor suppressor in the development of BE and EAC, at least in part through its effect on the Hh signaling pathway

Which clip? A prospective comparative study of retention rates of endoscopic clips on normal mucosa and ulcers in a porcine model

Background/Aim: There are currently no data on the relative retention rates of the Instinct clip, Resolution clip, and QuickClip2Long. Also, it is unknown whether retention rate differs when clips are applied to ulcerated rather than normal mucosa. The aim of this study is to compare the retention rates of three commonly used endoscopic clips. Materials and Methods: Six pigs underwent upper endoscopy with placement of one of each of the three types of clips on normal mucosa in the gastric body. Three mucosal resections were also performed to create "ulcers." Each ulcer was closed with placement of one of the three different clips. Repeat endoscopy was performed weekly for up to 4 weeks. Results: Only the Instinct and Resolution clips remained attached for the duration of the study (4 weeks). At each time point, a greater proportion of Instinct clips were retained on normal mucosa, followed by Resolution clips. QuickClip2Long had the lowest retention rate on normal mucosa. Similar retention rates of Instinct clips and Resolution clips were seen on simulated ulcers, although both were superior to QuickClip2Long. However, the difference did not reach statistical significance. All QuickClip2Long clips were dislodged at 4 weeks in both the groups. Conclusions: The Resolution and Instinct clips have comparable retention rates and both appeared to be better than the QuickClip2Long on normal mucosa-simulated ulcers; however this did not reach statistical significance. Both the Resolution clip and the Instinct clip may be preferred in clinical situations when long-term clip attachment is required, including marking of tumors for radiotherapy and anchoring feeding tubes or stents. Either of the currently available clips may be suitable for closure of iatrogenic mucosal defects without features of chronicity