Image Segmentation of Bacterial Cells in Biofilms

Bacterial biofilms are three-dimensional cell communities that live embedded in a self-produced extracellular matrix. Due to the protective properties of the dense coexistence of microorganisms, single bacteria inside the communities are hard to eradicate by antibacterial agents and bacteriophages. This increased resilience gives rise to severe problems in medical and technological settings. To fight the bacterial cells, an in-detail understanding of the underlying mechanisms of biofilm formation and development is required. Due to spatio-temporal variances in environmental conditions inside a single biofilm, the mechanisms can only be investigated by probing single-cells at different locations over time. Currently, the mechanistic information is primarily encoded in volumetric image data gathered with confocal fluorescence microscopy. To quantify features of the single-cell behaviour, single objects need to be detected. This identification of objects inside biofilm image data is called segmentation and is a key step for the understanding of the biological processes inside biofilms. In the first part of this work, a user-friendly computer program is presented which simplifies the analysis of bacterial biofilms. It provides a comprehensive set of tools to segment, analyse, and visualize fluorescent microscopy data without writing a single line of analysis code. This allows for faster feedback loops between experiment and analysis, and allows fast insights into the gathered data. The single-cell segmentation accuracy of a recent segmentation algorithm is discussed in detail. In this discussion, points for improvements are identified and a new optimized segmentation approach presented. The improved algorithm achieves superior segmentation accuracy on bacterial biofilms when compared to the current state-of-the-art algorithms. Finally, the possibility of deep learning-based end-to-end segmentation of biofilm data is investigated. A method for the quick generation of training data is presented and the results of two single-cell segmentation approaches for eukaryotic cells are adapted for the segmentation of bacterial biofilm segmentation.Bakterielle Biofilme sind drei-dimensionale Zellcluster, welche ihre eigene Matrix produzieren. Die selbst-produzierte Matrix bietet den Zellen einen gemeinschaftlichen Schutz vor äußeren Stressfaktoren. Diese Stressfaktoren können abiotischer Natur sein wie z.B. Temperatur- und Nährstoff\- schwankungen, oder aber auch biotische Faktoren wie z.B. Antibiotikabehandlung oder Bakteriophageninfektionen. Dies führt dazu, dass einzelne Zelle innerhalb der mikrobiologischen Gemeinschaften eine erhöhte Widerstandsfähigkeit aufweisen und eine große Herausforderung für Medizin und technische Anwendungen darstellen. Um Biofilme wirksam zu bekämpfen, muss man die dem Wachstum und Entwicklung zugrundeliegenden Mechanismen entschlüsseln. Aufgrund der hohen Zelldichte innerhalb der Gemeinschaften sind die Mechanismen nicht räumlich und zeitlich invariant, sondern hängen z.B. von Metabolit-, Nährstoff- und Sauerstoffgradienten ab. Daher ist es für die Beschreibung unabdingbar Beobachtungen auf Einzelzellebene durchzuführen. Für die nicht-invasive Untersuchung von einzelnen Zellen innerhalb eines Biofilms ist man auf konfokale Fluoreszenzmikroskopie angewiesen. Um aus den gesammelten, drei-dimensionalen Bilddaten Zelleigenschaften zu extrahieren, ist die Erkennung von den jeweiligen Zellen erforderlich. Besonders die digitale Rekonstruktion der Zellmorphologie spielt dabei eine große Rolle. Diese erhält man über die Segmentierung der Bilddaten. Dabei werden einzelne Bildelemente den abgebildeten Objekten zugeordnet. Damit lassen sich die einzelnen Objekte voneinander unterscheiden und deren Eigenschaften extrahieren. Im ersten Teil dieser Arbeit wird ein benutzerfreundliches Computerprogramm vorgestellt, welches die Segmentierung und Analyse von Fluoreszenzmikroskopiedaten wesentlich vereinfacht. Es stellt eine umfangreiche Auswahl an traditionellen Segmentieralgorithmen, Parameterberechnungen und Visualisierungsmöglichkeiten zur Verfügung. Alle Funktionen sind ohne Programmierkenntnisse zugänglich, sodass sie einer großen Gruppe von Benutzern zur Verfügung stehen. Die implementierten Funktionen ermöglichen es die Zeit zwischen durchgeführtem Experiment und vollendeter Datenanalyse signifikant zu verkürzen. Durch eine schnelle Abfolge von stetig angepassten Experimenten können in kurzer Zeit schnell wissenschaftliche Einblicke in Biofilme gewonnen werden.\\ Als Ergänzung zu den bestehenden Verfahren zur Einzelzellsegmentierung in Biofilmen, wird eine Verbesserung vorgestellt, welche die Genauigkeit von bisherigen Filter-basierten Algorithmen übertrifft und einen weiteren Schritt in Richtung von zeitlich und räumlich aufgelöster Einzelzellverfolgung innerhalb bakteriellen Biofilme darstellt. Abschließend wird die Möglichkeit der Anwendung von Deep Learning Algorithmen für die Segmentierung in Biofilmen evaluiert. Dazu wird eine Methode vorgestellt welche den Annotationsaufwand von Trainingsdaten im Vergleich zu einer vollständig manuellen Annotation drastisch verkürzt. Die erstellten Daten werden für das Training von Algorithmen eingesetzt und die Genauigkeit der Segmentierung an experimentellen Daten untersucht

Automated Olfactory Bulb Segmentation on High Resolutional T2-Weighted MRI

The neuroimage analysis community has neglected the automated segmentation of the olfactory bulb (OB) despite its crucial role in olfactory function. The lack of an automatic processing method for the OB can be explained by its challenging properties. Nonetheless, recent advances in MRI acquisition techniques and resolution have allowed raters to generate more reliable manual annotations. Furthermore, the high accuracy of deep learning methods for solving semantic segmentation problems provides us with an option to reliably assess even small structures. In this work, we introduce a novel, fast, and fully automated deep learning pipeline to accurately segment OB tissue on sub-millimeter T2-weighted (T2w) whole-brain MR images. To this end, we designed a three-stage pipeline: (1) Localization of a region containing both OBs using FastSurferCNN, (2) Segmentation of OB tissue within the localized region through four independent AttFastSurferCNN - a novel deep learning architecture with a self-attention mechanism to improve modeling of contextual information, and (3) Ensemble of the predicted label maps. The OB pipeline exhibits high performance in terms of boundary delineation, OB localization, and volume estimation across a wide range of ages in 203 participants of the Rhineland Study. Moreover, it also generalizes to scans of an independent dataset never encountered during training, the Human Connectome Project (HCP), with different acquisition parameters and demographics, evaluated in 30 cases at the native 0.7mm HCP resolution, and the default 0.8mm pipeline resolution. We extensively validated our pipeline not only with respect to segmentation accuracy but also to known OB volume effects, where it can sensitively replicate age effects

Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries

This two-volume set LNCS 12962 and 12963 constitutes the thoroughly refereed proceedings of the 7th International MICCAI Brainlesion Workshop, BrainLes 2021, as well as the RSNA-ASNR-MICCAI Brain Tumor Segmentation (BraTS) Challenge, the Federated Tumor Segmentation (FeTS) Challenge, the Cross-Modality Domain Adaptation (CrossMoDA) Challenge, and the challenge on Quantification of Uncertainties in Biomedical Image Quantification (QUBIQ). These were held jointly at the 23rd Medical Image Computing for Computer Assisted Intervention Conference, MICCAI 2020, in September 2021. The 91 revised papers presented in these volumes were selected form 151 submissions. Due to COVID-19 pandemic the conference was held virtually. This is an open access book

Towards deep unsupervised inverse graphics

Un objectif de longue date dans le domaine de la vision par ordinateur est de déduire le contenu 3D d’une scène à partir d’une seule photo, une tâche connue sous le nom d’inverse graphics. L’apprentissage automatique a, dans les dernières années, permis à de nombreuses approches de faire de grands progrès vers la résolution de ce problème. Cependant, la plupart de ces approches requièrent des données de supervision 3D qui sont coûteuses et parfois impossible à obtenir, ce qui limite les capacités d’apprentissage de telles œuvres. Dans ce travail, nous explorons l’architecture des méthodes d’inverse graphics non-supervisées et proposons deux méthodes basées sur des représentations 3D et algorithmes de rendus différentiables distincts: les surfels ainsi qu’une nouvelle représentation basée sur Voronoï. Dans la première méthode basée sur les surfels, nous montrons que, bien qu’efficace pour maintenir la cohérence visuelle, la production de surfels à l’aide d’une carte de profondeur apprise entraîne des ambiguïtés car la relation entre la carte de profondeur et le rendu n’est pas bijective. Dans notre deuxième méthode, nous introduisons une nouvelle représentation 3D basée sur les diagrammes de Voronoï qui modélise des objets/scènes à la fois explicitement et implicitement, combinant ainsi les avantages des deux approches. Nous montrons comment cette représentation peut être utilisée à la fois dans un contexte supervisé et non-supervisé et discutons de ses avantages par rapport aux représentations 3D traditionnellesA long standing goal of computer vision is to infer the underlying 3D content in a scene from a single photograph, a task known as inverse graphics. Machine learning has, in recent years, enabled many approaches to make great progress towards solving this problem. However, most approaches rely on 3D supervision data which is expensive and sometimes impossible to obtain and therefore limits the learning capabilities of such work. In this work, we explore the deep unsupervised inverse graphics training pipeline and propose two methods based on distinct 3D representations and associated differentiable rendering algorithms: namely surfels and a novel Voronoi-based representation. In the first method based on surfels, we show that, while effective at maintaining view-consistency, producing view-dependent surfels using a learned depth map results in ambiguities as the mapping between depth map and rendering is non-bijective. In our second method, we introduce a novel 3D representation based on Voronoi diagrams which models objects/scenes both explicitly and implicitly simultaneously, thereby combining the benefits of both. We show how this representation can be used in both a supervised and unsupervised context and discuss its advantages compared to traditional 3D representations

Template-free Articulated Neural Point Clouds for Reposable View Synthesis

Dynamic Neural Radiance Fields (NeRFs) achieve remarkable visual quality when synthesizing novel views of time-evolving 3D scenes. However, the common reliance on backward deformation fields makes reanimation of the captured object poses challenging. Moreover, the state of the art dynamic models are often limited by low visual fidelity, long reconstruction time or specificity to narrow application domains. In this paper, we present a novel method utilizing a point-based representation and Linear Blend Skinning (LBS) to jointly learn a Dynamic NeRF and an associated skeletal model from even sparse multi-view video. Our forward-warping approach achieves state-of-the-art visual fidelity when synthesizing novel views and poses while significantly reducing the necessary learning time when compared to existing work. We demonstrate the versatility of our representation on a variety of articulated objects from common datasets and obtain reposable 3D reconstructions without the need of object-specific skeletal templates. Code will be made available at https://github.com/lukasuz/Articulated-Point-NeRF

Dynamic Scene Reconstruction and Understanding

Traditional approaches to 3D reconstruction have achieved remarkable progress in static scene acquisition. The acquired data serves as priors or benchmarks for many vision and graphics tasks, such as object detection and robotic navigation. Thus, obtaining interpretable and editable representations from a raw monocular RGB-D video sequence is an outstanding goal in scene understanding. However, acquiring an interpretable representation becomes significantly more challenging when a scene contains dynamic activities; for example, a moving camera, rigid object movement, and non-rigid motions. These dynamic scene elements introduce a scene factorization problem, i.e., dividing a scene into elements and jointly estimating elements’ motion and geometry. Moreover, the monocular setting brings in the problems of tracking and fusing partially occluded objects as they are scanned from one viewpoint at a time. This thesis explores several ideas for acquiring an interpretable model in dynamic environments. Firstly, we utilize synthetic assets such as floor plans and object meshes to generate dynamic data for training and evaluation. Then, we explore the idea of learning geometry priors with an instance segmentation module, which predicts the location and grouping of indoor objects. We use the learned geometry priors to infer the occluded object geometry for tracking and reconstruction. While instance segmentation modules usually have a generalization issue, i.e., struggling to handle unknown objects, we observed that the empty space information in the background geometry is more reliable for detecting moving objects. Thus, we proposed a segmentation-by-reconstruction strategy for acquiring rigidly-moving objects and backgrounds. Finally, we present a novel neural representation to learn a factorized scene representation, reconstructing every dynamic element. The proposed model supports both rigid and non-rigid motions without pre-trained templates. We demonstrate that our systems and representation improve the reconstruction quality on synthetic test sets and real-world scans

Segmentation of pelvic structures from preoperative images for surgical planning and guidance

Prostate cancer is one of the most frequently diagnosed malignancies globally and the second leading cause of cancer-related mortality in males in the developed world. In recent decades, many techniques have been proposed for prostate cancer diagnosis and treatment. With the development of imaging technologies such as CT and MRI, image-guided procedures have become increasingly important as a means to improve clinical outcomes. Analysis of the preoperative images and construction of 3D models prior to treatment would help doctors to better localize and visualize the structures of interest, plan the procedure, diagnose disease and guide the surgery or therapy. This requires efficient and robust medical image analysis and segmentation technologies to be developed. The thesis mainly focuses on the development of segmentation techniques in pelvic MRI for image-guided robotic-assisted laparoscopic radical prostatectomy and external-beam radiation therapy. A fully automated multi-atlas framework is proposed for bony pelvis segmentation in MRI, using the guidance of MRI AE-SDM. With the guidance of the AE-SDM, a multi-atlas segmentation algorithm is used to delineate the bony pelvis in a new \ac{MRI} where there is no CT available. The proposed technique outperforms state-of-the-art algorithms for MRI bony pelvis segmentation. With the SDM of pelvis and its segmented surface, an accurate 3D pelvimetry system is designed and implemented to measure a comprehensive set of pelvic geometric parameters for the examination of the relationship between these parameters and the difficulty of robotic-assisted laparoscopic radical prostatectomy. This system can be used in both manual and automated manner with a user-friendly interface. A fully automated and robust multi-atlas based segmentation has also been developed to delineate the prostate in diagnostic MR scans, which have large variation in both intensity and shape of prostate. Two image analysis techniques are proposed, including patch-based label fusion with local appearance-specific atlases and multi-atlas propagation via a manifold graph on a database of both labeled and unlabeled images when limited labeled atlases are available. The proposed techniques can achieve more robust and accurate segmentation results than other multi-atlas based methods. The seminal vesicles are also an interesting structure for therapy planning, particularly for external-beam radiation therapy. As existing methods fail for the very onerous task of segmenting the seminal vesicles, a multi-atlas learning framework via random decision forests with graph cuts refinement has further been proposed to solve this difficult problem. Motivated by the performance of this technique, I further extend the multi-atlas learning to segment the prostate fully automatically using multispectral (T1 and T2-weighted) MR images via hybrid \ac{RF} classifiers and a multi-image graph cuts technique. The proposed method compares favorably to the previously proposed multi-atlas based prostate segmentation. The work in this thesis covers different techniques for pelvic image segmentation in MRI. These techniques have been continually developed and refined, and their application to different specific problems shows ever more promising results.Open Acces

Visual Perception For Robotic Spatial Understanding

Humans understand the world through vision without much effort. We perceive the structure, objects, and people in the environment and pay little direct attention to most of it, until it becomes useful. Intelligent systems, especially mobile robots, have no such biologically engineered vision mechanism to take for granted. In contrast, we must devise algorithmic methods of taking raw sensor data and converting it to something useful very quickly. Vision is such a necessary part of building a robot or any intelligent system that is meant to interact with the world that it is somewhat surprising we don\u27t have off-the-shelf libraries for this capability. Why is this? The simple answer is that the problem is extremely difficult. There has been progress, but the current state of the art is impressive and depressing at the same time. We now have neural networks that can recognize many objects in 2D images, in some cases performing better than a human. Some algorithms can also provide bounding boxes or pixel-level masks to localize the object. We have visual odometry and mapping algorithms that can build reasonably detailed maps over long distances with the right hardware and conditions. On the other hand, we have robots with many sensors and no efficient way to compute their relative extrinsic poses for integrating the data in a single frame. The same networks that produce good object segmentations and labels in a controlled benchmark still miss obvious objects in the real world and have no mechanism for learning on the fly while the robot is exploring. Finally, while we can detect pose for very specific objects, we don\u27t yet have a mechanism that detects pose that generalizes well over categories or that can describe new objects efficiently. We contribute algorithms in four of the areas mentioned above. First, we describe a practical and effective system for calibrating many sensors on a robot with up to 3 different modalities. Second, we present our approach to visual odometry and mapping that exploits the unique capabilities of RGB-D sensors to efficiently build detailed representations of an environment. Third, we describe a 3-D over-segmentation technique that utilizes the models and ego-motion output in the previous step to generate temporally consistent segmentations with camera motion. Finally, we develop a synthesized dataset of chair objects with part labels and investigate the influence of parts on RGB-D based object pose recognition using a novel network architecture we call PartNet

3D CNN methods in biomedical image segmentation

A definite trend in Biomedical Imaging is the one towards the integration of increasingly complex interpretative layers to the pure data acquisition process. One of the most interesting and looked-forward goals in the field is the automatic segmentation of objects of interest in extensive acquisition data, target that would allow Biomedical Imaging to look beyond its use as a purely assistive tool to become a cornerstone in ambitious large-scale challenges like the extensive quantitative study of the Human Brain. In 2019 Convolutional Neural Networks represent the state of the art in Biomedical Image segmentation and scientific interests from a variety of fields, spacing from automotive to natural resource exploration, converge to their development. While most of the applications of CNNs are focused on single-image segmentation, biomedical image data -being it MRI, CT-scans, Microscopy, etc- often benefits from three-dimensional volumetric expression. This work explores a reformulation of the CNN segmentation problem that is native to the 3D nature of the data, with particular interest to the applications to Fluorescence Microscopy volumetric data produced at the European Laboratories for Nonlinear Spectroscopy in the context of two different large international human brain study projects: the Human Brain Project and the White House BRAIN Initiative

Characterization of multiphase flows integrating X-ray imaging and virtual reality

Multiphase flows are used in a wide variety of industries, from energy production to pharmaceutical manufacturing. However, because of the complexity of the flows and difficulty measuring them, it is challenging to characterize the phenomena inside a multiphase flow. To help overcome this challenge, researchers have used numerous types of noninvasive measurement techniques to record the phenomena that occur inside the flow. One technique that has shown much success is X-ray imaging. While capable of high spatial resolutions, X-ray imaging generally has poor temporal resolution. This research improves the characterization of multiphase flows in three ways. First, an X-ray image intensifier is modified to use a high-speed camera to push the temporal limits of what is possible with current tube source X-ray imaging technology. Using this system, sample flows were imaged at 1000 frames per second without a reduction in spatial resolution. Next, the sensitivity of X-ray computed tomography (CT) measurements to changes in acquisition parameters is analyzed. While in theory CT measurements should be stable over a range of acquisition parameters, previous research has indicated otherwise. The analysis of this sensitivity shows that, while raw CT values are strongly affected by changes to acquisition parameters, if proper calibration techniques are used, acquisition parameters do not significantly influence the results for multiphase flow imaging. Finally, two algorithms are analyzed for their suitability to reconstruct an approximate tomographic slice from only two X-ray projections. These algorithms increase the spatial error in the measurement, as compared to traditional CT; however, they allow for very high temporal resolutions for 3D imaging. The only limit on the speed of this measurement technique is the image intensifier-camera setup, which was shown to be capable of imaging at a rate of at least 1000 FPS. While advances in measurement techniques for multiphase flows are one part of improving multiphase flow characterization, the challenge extends beyond measurement techniques. For improved measurement techniques to be useful, the data must be accessible to scientists in a way that maximizes the comprehension of the phenomena. To this end, this work also presents a system for using the Microsoft Kinect sensor to provide natural, non-contact interaction with multiphase flow data. Furthermore, this system is constructed so that it is trivial to add natural, non-contact interaction to immersive visualization applications. Therefore, multiple visualization applications can be built that are optimized to specific types of data, but all leverage the same natural interaction. Finally, the research is concluded by proposing a system that integrates the improved X-ray measurements, with the Kinect interaction system, and a CAVE automatic virtual environment (CAVE) to present scientists with the multiphase flow measurements in an intuitive and inherently three-dimensional manner