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Solutions to vision tasks in gastrointestinal endoscopy (GIE) conventionally use image encoders pretrained in a supervised manner with ImageNet-1k as backbones. However, the use of modern self-supervised pretraining algorithms and a recent dataset of 100k unlabelled GIE images (Hyperkvasir-unlabelled) may allow for improvements. In this work, we study the fine-tuned performance of models with ResNet50 and ViT-B backbones pretrained in self-supervised and supervised manners with ImageNet-1k and Hyperkvasir-unlabelled (self-supervised only) in a range of GIE vision tasks. In addition to identifying the most suitable pretraining pipeline and backbone architecture for each task, out of those considered, our results suggest three general principles. Firstly, that self-supervised pretraining generally produces more suitable backbones for GIE vision tasks than supervised pretraining. Secondly, that self-supervised pretraining with ImageNet-1k is typically more suitable than pretraining with Hyperkvasir-unlabelled, with the notable exception of monocular depth estimation in colonoscopy. Thirdly, that ViT-Bs are more suitable in polyp segmentation and monocular depth estimation in colonoscopy, ResNet50s are more suitable in polyp detection, and both architectures perform similarly in anatomical landmark recognition and pathological finding characterisation. We hope this work draws attention to the complexity of pretraining for GIE vision tasks, informs this development of more suitable approaches than the convention, and inspires further research on this topic to help advance this development. Code available: https://www.github.com/ESandML/SSL4GIE.

Most vision-based 3D pose estimation approaches typically rely on knowledge of object’s 3D model, depth measurements, and often require time-consuming iterative refinement to improve accuracy. However, these can be seen as limiting factors for broader real-life applications. The main motivation for this paper is to address these limitations. To solve this, a novel Convolutional Variational Auto-Encoder based Multi-Level Network for object 3D pose estimation (CVML-Pose) method is proposed. Unlike most other methods, the proposed CVML-Pose implicitly learns an object’s 3D pose from only RGB images encoded in its latent space without knowing the object’s 3D model, depth information, or performing a post-refinement. CVML-Pose consists of two main modules: (i) CVML-AE representing convolutional variational autoencoder, whose role is to extract features from RGB images, (ii) Multi-Layer Perceptron and K-Nearest Neighbor regressors mapping the latent variables to object 3D pose including, respectively, rotation and translation. The proposed CVML-Pose has been evaluated on the LineMod and LineMod-Occlusion benchmark datasets. It has been shown to outperform other methods based on latent representations and achieves comparable results to the state-of-the-art, but without use of a 3D model or depth measurements. Utilizing the t-Distributed Stochastic Neighbor Embedding algorithm, the CVML-Pose latent space is shown to successfully represent objects’ category and topology. This opens up a prospect of integrated estimation of pose and other attributes (possibly also including surface finish or shape variations), which, with real-time processing due to the absence of iterative refinement, can facilitate various robotic applications. Code available: https://github.com/JZhao12/CVML-Pose.

The THO complex participates during eukaryotic mRNA biogenesis in coupling transcription to formation and nuclear export of translation-competent messenger ribonucleoprotein particles. In Saccharomyces cerevisiae, THO has been defined as a heteropentamer composed of the Tho2p, Hpr1p, Tex1p, Mft1p, and Thp2p subunits and the overall three-dimensional shape of the complex has been established by negative stain electron microscopy. Here, we use small-angle X-ray scattering measured for isolated THO components (Mft1p and Thp2p) as well as THO subcomplexes (Mft1p-Thp2p and Mft1p-Thp2p-Tho2p) to construct structural building blocks that allow positioning of each subunit within the complex. To accomplish this, the individual envelopes determined for Mft1p and Thp2p are first fitted inside those of the Mft1p-Thp2p and Mft1p-Thp2p-Tho2p complexes. Next, the ternary complex structure is placed in the context of the five-component electron microscopy structure. Our model reveals not only the position of each protein in the THO complex relative to each other, but also shows that the pentamer is likely somewhat larger than what was observed by electron microscopy.