Most commercially available haptic gloves compromise the accuracy of hand-posture measurements in favor of a simpler design with fewer sensors. While inaccurate posture data is often sufficient for the task at hand in biomedical settings such as VR-therapy-aided rehabilitation, measurements should be as precise as possible to digitally recreate hand postures as accurately as possible. With these applications in mind, we have added extra sensors to the commercially available Dexmo haptic glove by Dexta Robotics and applied kinematic models of the haptic glove and the user's hand to improve the accuracy of hand-posture measurements. In this work, we describe the augmentations and the kinematic modeling approach. Additionally, we present and discuss an evaluation of hand posture measurements as a proof of concept.

The rapid pace of innovation in biological microscopy imaging has led to large images, putting pressure on data storage and impeding efficient sharing, management, and visualization. This necessitates the development of efficient compression solutions. Traditional CODEC methods struggle to adapt to the diverse bioimaging data and often suffer from sub-optimal compression. In this study, we propose an adaptive compression workflow based on Implicit Neural Representation (INR). This approach permits application-specific compression objectives, capable of compressing images of any shape and arbitrary pixel-wise decompression. We demonstrated on a wide range of microscopy images from real applications that our workflow not only achieved high, controllable compression ratios (e.g., 512x) but also preserved detailed information critical for downstream analysis.

With the fast development of modern microscopes and bioimaging techniques, an unprecedentedly large amount of imaging data are being generated, stored, analyzed, and even shared through networks. The size of the data poses great challenges for current data infrastructure. One common way to reduce the data size is by image compression. This present study analyzes classic and deep learning based image compression methods, and their impact on deep learning based image processing models. Deep learning based label-free prediction models (i.e., predicting fluorescent images from bright field images) are used as an example application for comparison and analysis. Effective image compression methods could help reduce the data size significantly without losing necessary information, and therefore reduce the burden on data management infrastructure and permit fast transmission through the network for data sharing or cloud computing. To compress images in such a wanted way, multiple classical lossy image compression techniques are compared to several AI-based compression models provided by and trained with the CompressAI toolbox using python. These different compression techniques are compared in compression ratio, multiple image similarity measures and, most importantly, the prediction accuracy from label-free models on compressed images. We found that AI-based compression techniques largely outperform the classic ones and will minimally affect the downstream label-free task in 2D cases. In the end, we hope the present study could shed light on the potential of deep learning based image compression and the impact of image compression on downstream deep learning based image analysis models.

Prior to the deep learning era, shape was commonly used to describe the objects. Nowadays, state-of-the-art (SOTA) algorithms in medical imaging are predominantly diverging from computer vision, where voxel grids, meshes, point clouds, and implicit surface models are used. This is seen from numerous shape-related publications in premier vision conferences as well as the growing popularity of ShapeNet (about 51,300 models) and Princeton ModelNet (127,915 models). For the medical domain, we present a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D models of surgical instrument, called MedShapeNet, created to facilitate the translation of data-driven vision algorithms to medical applications and to adapt SOTA vision algorithms to medical problems. As a unique feature, we directly model the majority of shapes on the imaging data of real patients. As of today, MedShapeNet includes 23 dataset with more than 100,000 shapes that are paired with annotations (ground truth). Our data is freely accessible via a web interface and a Python application programming interface (API) and can be used for discriminative, reconstructive, and variational benchmarks as well as various applications in virtual, augmented, or mixed reality, and 3D printing. Exemplary, we present use cases in the fields of classification of brain tumors, facial and skull reconstructions, multi-class anatomy completion, education, and 3D printing. In future, we will extend the data and improve the interfaces. The project pages are: https://medshapenet.ikim.nrw/ and https://github.com/Jianningli/medshapenet-feedback

Artificial intelligence (AI) has been widely used in bioimage image analysis nowadays, but the efficiency of AI models, like the energy consumption and latency is not ignorable due to the growing model size and complexity, as well as the fast-growing analysis needs in modern biomedical studies. In this work, we present EfficientBioAI, a plug-and-play toolbox that can compress given bioimaging AI models for them to run with significantly reduced energy cost and inference time on both CPU and GPU, without compromise on accuracy. In some cases, the prediction accuracy could even increase after compression, since the compression procedure could remove redundant information in the model representation and therefore reduce over-fitting. From four different bioimage analysis applications, we observed around 2-5 times speed-up during inference and 30-80% saving in energy. Cutting the runtime of large scale bioimage analysis from days to hours or getting a two-minutes bioimaging AI model inference done in near real-time will open new doors for method development and biomedical discoveries. Over the last decade, microscopy bioimaging techniques have been advancing at unprecedented pace, with higher spatial resolution [1], larger imaging volumes [2] and higher throughput for screening [3]. These advancements have also led to the rapid development of artificial intelligence (AI) methods in microscopy image analysis tools (e.g. As the AI-based microscopy image analysis methods setting new records in various benchmarks and permitting quantitative biological studies not feasible before, we want to raise the awareness of another aspect of bioimaging AI models' performance: efficiency.

Segmentation of 3D images is a fundamental problem in biomedical image analysis. Deep learning (DL) approaches have achieved the state-of-the-art segmentation performance. To exploit the 3D contexts using neural networks, known DL segmentation methods, including 3D convolution, 2D convolution on the planes orthogonal to 2D slices, and LSTM in multiple directions, all suffer incompatibility with the highly anisotropic dimensions in common 3D biomedical images. In this paper, we propose a new DL framework for 3D image segmentation, based on a combination of a fully convolutional network (FCN) and a recurrent neural network (RNN), which are responsible for exploiting the intra-slice and inter-slice contexts, respectively. To our best knowledge, this is the first DL framework for 3D image segmentation that explicitly leverages 3D image anisotropism. Evaluating using a dataset from the ISBI Neuronal Structure Segmentation Challenge and in-house image stacks for 3D fungus segmentation, our approach achieves promising results, comparing to the known DL-based 3D segmentation approaches.