In this paper, we propose a hybrid approach for multi-object microbial cell segmentation. The approach combines an ML-based detection with a geometry-aware variational-based segmentation using B-splines that are parametrized based on a geometric model of the cell shape. The detection is done first using YOLOv5. In a second step, each detected cell is segmented individually. Thus, the segmentation only needs to be done on a per-cell basis, which makes it amenable to a variational approach that incorporates prior knowledge on the geometry. Here, the contour of the segmentation is modelled as closed uniform cubic B-spline, whose control points are parametrized using the known cell geometry. Compared to purely ML-based segmentation approaches, which need accurate segmentation maps as training data that are very laborious to produce, our method just needs bounding boxes as training data. Still, the proposed method performs on par with ML-based segmentation approaches usually used in this context. We study the performance of the proposed method on time-lapse microscopy data of Corynebacterium glutamicum.
SINTEF（辛泰夫研究院）；Oslo University Hospital（奥斯陆大学医院）；The Intervention Centre（介入中心）
We propose a novel approach to image segmentation based on combining implicit spline representations with deep convolutional neural networks. This is done by predicting the control points of a bivariate spline function whose zero-set represents the segmentation boundary. We adapt several existing neural network architectures and design novel loss functions that are tailored towards providing implicit spline curve approximations. The method is evaluated on a congenital heart disease computed tomography medical imaging dataset. Experiments are carried out by measuring performance in various stan…
We here propose an automated pipeline for the microscopy image-based characterization of catalytically active inclusion bodies (CatIBs), which includes a fully automatic experimental high-throughput workflow combined with a hybrid approach for multi-object microbial cell segmentation. For automated microscopy, a CatIB producer strain was cultivated in a microbioreactor from which samples were injected into a flow chamber. The flow chamber was fixed under a microscope and an integrated camera took a series of images per sample. To explore heterogeneity of CatIB development during the cultivatio…
Bruch's membrane (BM) segmentation on optical coherence tomography (OCT) is a pivotal step for the diagnosis and follow-up of age-related macular degeneration (AMD), one of the leading causes of blindness in the developed world. Automated BM segmentation methods exist, but they usually do not account for the anatomical coherence of the results, neither provide feedback on the confidence of the prediction. These factors limit the applicability of these systems in real-world scenarios. With this in mind, we propose an end-to-end deep learning method for automated BM segmentation in AMD patients.…
Segmentation of 3D pore space from CT images using curvilinear skeleton: application to numerical simulation of microbial decomposition
IRD（法国发展研究院）；UMMISCO（复杂系统数学与信息建模单元）；Cadi Ayyad University（卡迪·阿亚德大学）；Faculty of Sciences Semlalia（塞姆拉利亚科学学院）；LIB（自由研究所）；UFR Sciences et Techniques（科学与技术培训与研究单位）；University of Burgundy（勃艮第大学）；INRA（法国国家农业研究院）
University Hospitals Leuven（鲁汶大学医院）；King’s College London（伦敦国王学院）；KU Leuven（鲁汶大学）；INESC TEC - Institute for Systems and Computer Engineering, Technology and Science（INESC TEC - 系统与计算机工程、技术与科学研究所）
Automatic medical image segmentation via convolutional neural networks (CNNs) has shown promising results. However, they may not always be robust enough for clinical use. Sub-optimal segmentation would require clinician's to manually delineate the target object, causing frustration. To address this problem, a novel interactive CNN-based segmentation framework is proposed in this work. The aim is to represent the CNN segmentation contour as B-splines by utilising B-spline explicit active surfaces (BEAS). The interactive element of the framework allows the user to precisely edit the contour in r…
NeuroSYS（NeuroSYS公司）；Wroclaw University of Science and Technology（弗罗茨瓦夫科技大学）
We introduce an effective strategy to generate an annotated synthetic dataset of microbiological images of Petri dishes that can be used to train deep learning models in a fully supervised fashion. The developed generator employs traditional computer vision algorithms together with a neural style transfer method for data augmentation. We show that the method is able to synthesize a dataset of realistic looking images that can be used to train a neural network model capable of localising, segmenting, and classifying five different microbial species. Our method requires significantly fewer resou…
While robotic manipulation of rigid objects is quite straightforward, coping with deformable objects is an open issue. More specifically, tasks like tying a knot, wiring a connector or even surgical suturing deal with the domain of Deformable Linear Objects (DLOs). In particular the detection of a DLO is a non-trivial problem especially under clutter and occlusions (as well as self-occlusions). The pose estimation of a DLO results into the identification of its parameters related to a designed model, e.g. a basis spline. It follows that the stand-alone segmentation of a DLO might not be suffic…
AD-GS: Object-Aware B-Spline Gaussian Splatting for Self-Supervised Autonomous Driving
College of Computer Science, Nankai University（南开大学计算机科学学院）；University of Illinois Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）；School of Intelligence Science and Technology, Nanjing University（南京大学智能科学与技术学院）
Universidad Politécnica de Madrid（马德里理工大学）；École Polytechnique Fédérale de Lausanne (EPFL)（洛桑联邦理工学院）；Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN)（生物工程、生物材料与纳米医学生物医学研究网络中心）；University of Lausanne（洛桑大学）
Closer to Ground Truth: Realistic Shape and Appearance Labeled Data Generation for Unsupervised Underwater Image Segmentation
NORCE Norwegian Research Center AS（NORCE挪威研究中心）；National University of Science and Technology "Politehnica" Bucharest（布加勒斯特理工科学技术大学）；"Simion Stoilow" Institute of Mathematics of the Romanian Academy（罗马尼亚科学院西米翁斯托伊洛夫数学研究所）
When Swin Transformer Meets KANs: An Improved Transformer Architecture for Medical Image Segmentation
Department of Computer Science and Engineering, University of Notre Dame（计算机科学与工程系，诺丁汉大学）；Department of Computer Science, University of Texas Rio Grande Valley（计算机科学系，德克萨斯大学里奥格兰德谷分校）
Boston Children's Hospital（波士顿儿童医院）；Harvard Medical School（哈佛医学院）；Northeastern University（东北大学）
Fully convolutional deep neural networks have been asserted to be fast and precise frameworks with great potential in image segmentation. One of the major challenges in training such networks raises when data is unbalanced, which is common in many medical imaging applications such as lesion segmentation where lesion class voxels are often much lower in numbers than non-lesion voxels. A trained network with unbalanced data may make predictions with high precision and low recall, being severely biased towards the non-lesion class which is particularly undesired in most medical applications where…
Object detection is a critical part of visual scene understanding. The representation of the object in the detection task has important implications on the efficiency and feasibility of annotation, robustness to occlusion, pose, lighting, and other visual sources of semantic uncertainty, and effectiveness in real-world applications (e.g., autonomous driving). Popular object representations include 2D and 3D bounding boxes, polygons, splines, pixels, and voxels. Each have their strengths and weakness. In this work, we propose a new representation of objects based on the bivariate normal distrib…
Fluorescence microscopy is a widely used method among cell biologists for studying the localization and co-localization of fluorescent protein. For microbial cell biologists, these studies often include tedious and time-consuming manual segmentation of bacteria and of the fluorescence clusters or working with multiple programs. Here, we present MicroAnalyzer - a tool that automates these tasks by providing an end-to-end platform for microscope image analysis. While such tools do exist, they are costly, black-boxed programs. Microanalyzer offers an open-source alternative to these tools, allowi…
EAP4EMSIG -- Enhancing Event-Driven Microscopy for Microfluidic Single-Cell Analysis
Institute for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology（自动化与应用信息研究所，卡尔斯鲁厄理工学院）；Institute of Biological and Chemical Systems (IBCS), Karlsruhe Institute of Technology（生物与化学系统研究所，卡尔斯鲁厄理工学院）；Institute for Data Science and Machine Learning (IAS-8), Forschungszentrum Jülich GmbH（数据科学与机器学习研究所，吕内堡研究中心 GmbH）；Institute of Bio- and Geosciences (IBG-1), Forschungszentrum Jülich GmbH（生物与地球科学研究所，吕内堡研究中心 GmbH）；Computational Systems Biology (AVT-CSB), RWTH Aachen University（计算系统生物学（AVT-CSB），亚琛工业大学）
Lane detection is typically tackled with a two-step pipeline in which a segmentation mask of the lane markings is predicted first, and a lane line model (like a parabola or spline) is fitted to the post-processed mask next. The problem with such a two-step approach is that the parameters of the network are not optimized for the true task of interest (estimating the lane curvature parameters) but for a proxy task (segmenting the lane markings), resulting in sub-optimal performance. In this work, we propose a method to train a lane detector in an end-to-end manner, directly regressing the lane p…
