Parcellation of Visual Cortex on high-resolution histological Brain Sections using Convolutional Neural Networks

Microscopic analysis of histological sections is considered the "gold standard" to verify structural parcellations in the human brain. Its high resolution allows the study of laminar and columnar patterns of cell distributions, which build an important basis for the simulation of cortical areas and networks. However, such cytoarchitectonic mapping is a semiautomatic, time consuming process that does not scale with high throughput imaging. We present an automatic approach for parcellating histological sections at 2um resolution. It is based on a convolutional neural network that combines topological information from probabilistic atlases with the texture features learned from high-resolution cell-body stained images. The model is applied to visual areas and trained on a sparse set of partial annotations. We show how predictions are transferable to new brains and spatially consistent across sections.Comment: Accepted for oral presentation at International Symposium of Biomedical Imaging (ISBI) 201

Rapid Online Analysis of Local Feature Detectors and Their Complementarity

A vision system that can assess its own performance and take appropriate actions online to maximize its effectiveness would be a step towards achieving the long-cherished goal of imitating humans. This paper proposes a method for performing an online performance analysis of local feature detectors, the primary stage of many practical vision systems. It advocates the spatial distribution of local image features as a good performance indicator and presents a metric that can be calculated rapidly, concurs with human visual assessments and is complementary to existing offline measures such as repeatability. The metric is shown to provide a measure of complementarity for combinations of detectors, correctly reflecting the underlying principles of individual detectors. Qualitative results on well-established datasets for several state-of-the-art detectors are presented based on the proposed measure. Using a hypothesis testing approach and a newly-acquired, larger image database, statistically-significant performance differences are identified. Different detector pairs and triplets are examined quantitatively and the results provide a useful guideline for combining detectors in applications that require a reasonable spatial distribution of image features. A principled framework for combining feature detectors in these applications is also presented. Timing results reveal the potential of the metric for online applications. © 2013 by the authors; licensee MDPI, Basel, Switzerland

Robust Wide-Baseline Stereo Matching for Sparsely Textured Scenes

The task of wide baseline stereo matching algorithms is to identify corresponding elements in pairs of overlapping images taken from significantly different viewpoints. Such algorithms are a key ingredient to many computer vision applications, including object recognition, automatic camera orientation, 3D reconstruction and image registration. Although today's methods for wide baseline stereo matching produce reliable results for typical application scenarios, they assume properties of the image data that are not always granted, for example a significant amount of distinctive surface texture. For such problems, highly advanced algorithms have been proposed, which are often very problem specific, difficult to implement and hard to transfer to new matching problems. The motivation for our work comes from the belief that we can find a generic formulation for robust wide baseline image matching that is able to solve difficult matching problems and at the same time applicable to a variety of applications. It should be easy to implement, and have good semantic interpretability. Therefore our key contribution is the development of a generic statistical model for wide baseline stereo matching, which seamlessly integrates different types of image features, similarity measures and spatial feature relationships as information cues. It unifies the ideas of existing approaches into a Bayesian formulation, which has a clear statistical interpretation as the MAP estimate of a binary classification problem. The model ultimately takes the form of a global minimization problem that can be solved with standard optimization techniques. The particular type of features, measures, and spatial relationships however is not prescribed. A major advantage of our model over existing approaches is its ability to compensate weaknesses in one information cue implicitly by exploiting the strength of others. In our experiments we concentrate on images of sparsely textured scenes as a specifically difficult matching problem. Here the amount of stable image features is typically rather small, and the distinctiveness of feature descriptions often low. We use the proposed framework to implement a wide baseline stereo matching algorithm that can deal better with poor texture than established methods. For demonstrating the practical relevance, we also apply this algorithm to a system for automatic image orientation. Here, the task is to reconstruct the relative 3D positions and orientations of the cameras corresponding to a set of overlapping images. We show that our implementation leads to more successful results in case of sparsely textured scenes, while still retaining state of the art performance on standard datasets.Robuste Merkmalszuordnung für Bildpaare schwach texturierter Szenen mit deutlicher Stereobasis Die Aufgabe von Wide Baseline Stereo Matching Algorithmen besteht darin, korrespondierende Elemente in Paaren überlappender Bilder mit deutlich verschiedenen Kamerapositionen zu bestimmen. Solche Algorithmen sind ein grundlegender Baustein für zahlreiche Computer Vision Anwendungen wie Objekterkennung, automatische Kameraorientierung, 3D Rekonstruktion und Bildregistrierung. Die heute etablierten Verfahren für Wide Baseline Stereo Matching funktionieren in typischen Anwendungsszenarien sehr zuverlässig. Sie setzen jedoch Eigenschaften der Bilddaten voraus, die nicht immer gegeben sind, wie beispielsweise einen hohen Anteil markanter Textur. Für solche Fälle wurden sehr komplexe Verfahren entwickelt, die jedoch oft nur auf sehr spezifische Probleme anwendbar sind, einen hohen Implementierungsaufwand erfordern, und sich zudem nur schwer auf neue Matchingprobleme übertragen lassen. Die Motivation für diese Arbeit entstand aus der Überzeugung, dass es eine möglichst allgemein anwendbare Formulierung für robustes Wide Baseline Stereo Matching geben muß, die sich zur Lösung schwieriger Zuordnungsprobleme eignet und dennoch leicht auf verschiedenartige Anwendungen angepasst werden kann. Sie sollte leicht implementierbar sein und eine hohe semantische Interpretierbarkeit aufweisen. Unser Hauptbeitrag besteht daher in der Entwicklung eines allgemeinen statistischen Modells für Wide Baseline Stereo Matching, das verschiedene Typen von Bildmerkmalen, Ähnlichkeitsmaßen und räumlichen Beziehungen nahtlos als Informationsquellen integriert. Es führt Ideen bestehender Lösungsansätze in einer Bayes'schen Formulierung zusammen, die eine klare Interpretation als MAP Schätzung eines binären Klassifikationsproblems hat. Das Modell nimmt letztlich die Form eines globalen Minimierungsproblems an, das mit herkömmlichen Optimierungsverfahren gelöst werden kann. Der konkrete Typ der verwendeten Bildmerkmale, Ähnlichkeitsmaße und räumlichen Beziehungen ist nicht explizit vorgeschrieben. Ein wichtiger Vorteil unseres Modells gegenüber vergleichbaren Verfahren ist seine Fähigkeit, Schwachpunkte einer Informationsquelle implizit durch die Stärken anderer Informationsquellen zu kompensieren. In unseren Experimenten konzentrieren wir uns insbesondere auf Bilder schwach texturierter Szenen als ein Beispiel schwieriger Zuordnungsprobleme. Die Anzahl stabiler Bildmerkmale ist hier typischerweise gering, und die Unterscheidbarkeit der Merkmalsbeschreibungen schlecht. Anhand des vorgeschlagenen Modells implementieren wir einen konkreten Wide Baseline Stereo Matching Algorithmus, der besser mit schwacher Textur umgehen kann als herkömmliche Verfahren. Um die praktische Relevanz zu verdeutlichen, wenden wir den Algorithmus für die automatische Bildorientierung an. Hier besteht die Aufgabe darin, zu einer Menge überlappender Bilder die relativen 3D Kamerapositionen und Kameraorientierungen zu bestimmen. Wir zeigen, dass der Algorithmus im Fall schwach texturierter Szenen bessere Ergebnisse als etablierte Verfahren ermöglicht, und dennoch bei Standard-Datensätzen vergleichbare Ergebnisse liefert

Robust Wide-Baseline Stereo Matching for Sparsely Textured Scenes

The task of wide baseline stereo matching algorithms is to identify corresponding elements in pairs of overlapping images taken from significantly different viewpoints. Such algorithms are a key ingredient to many computer vision applications, including object recognition, automatic camera orientation, 3D reconstruction and image registration. Although today's methods for wide baseline stereo matching produce reliable results for typical application scenarios, they assume properties of the image data that are not always granted, for example a significant amount of distinctive surface texture. For such problems, highly advanced algorithms have been proposed, which are often very problem specific, difficult to implement and hard to transfer to new matching problems. The motivation for our work comes from the belief that we can find a generic formulation for robust wide baseline image matching that is able to solve difficult matching problems and at the same time applicable to a variety of applications. It should be easy to implement, and have good semantic interpretability. Therefore our key contribution is the development of a generic statistical model for wide baseline stereo matching, which seamlessly integrates different types of image features, similarity measures and spatial feature relationships as information cues. It unifies the ideas of existing approaches into a Bayesian formulation, which has a clear statistical interpretation as the MAP estimate of a binary classification problem. The model ultimately takes the form of a global minimization problem that can be solved with standard optimization techniques. The particular type of features, measures, and spatial relationships however is not prescribed. A major advantage of our model over existing approaches is its ability to compensate weaknesses in one information cue implicitly by exploiting the strength of others. In our experiments we concentrate on images of sparsely textured scenes as a specifically difficult matching problem. Here the amount of stable image features is typically rather small, and the distinctiveness of feature descriptions often low. We use the proposed framework to implement a wide baseline stereo matching algorithm that can deal better with poor texture than established methods. For demonstrating the practical relevance, we also apply this algorithm to a system for automatic image orientation. Here, the task is to reconstruct the relative 3D positions and orientations of the cameras corresponding to a set of overlapping images. We show that our implementation leads to more successful results in case of sparsely textured scenes, while still retaining state of the art performance on standard datasets.Robuste Merkmalszuordnung für Bildpaare schwach texturierter Szenen mit deutlicher Stereobasis Die Aufgabe von Wide Baseline Stereo Matching Algorithmen besteht darin, korrespondierende Elemente in Paaren überlappender Bilder mit deutlich verschiedenen Kamerapositionen zu bestimmen. Solche Algorithmen sind ein grundlegender Baustein für zahlreiche Computer Vision Anwendungen wie Objekterkennung, automatische Kameraorientierung, 3D Rekonstruktion und Bildregistrierung. Die heute etablierten Verfahren für Wide Baseline Stereo Matching funktionieren in typischen Anwendungsszenarien sehr zuverlässig. Sie setzen jedoch Eigenschaften der Bilddaten voraus, die nicht immer gegeben sind, wie beispielsweise einen hohen Anteil markanter Textur. Für solche Fälle wurden sehr komplexe Verfahren entwickelt, die jedoch oft nur auf sehr spezifische Probleme anwendbar sind, einen hohen Implementierungsaufwand erfordern, und sich zudem nur schwer auf neue Matchingprobleme übertragen lassen. Die Motivation für diese Arbeit entstand aus der Überzeugung, dass es eine möglichst allgemein anwendbare Formulierung für robustes Wide Baseline Stereo Matching geben muß, die sich zur Lösung schwieriger Zuordnungsprobleme eignet und dennoch leicht auf verschiedenartige Anwendungen angepasst werden kann. Sie sollte leicht implementierbar sein und eine hohe semantische Interpretierbarkeit aufweisen. Unser Hauptbeitrag besteht daher in der Entwicklung eines allgemeinen statistischen Modells für Wide Baseline Stereo Matching, das verschiedene Typen von Bildmerkmalen, Ähnlichkeitsmaßen und räumlichen Beziehungen nahtlos als Informationsquellen integriert. Es führt Ideen bestehender Lösungsansätze in einer Bayes'schen Formulierung zusammen, die eine klare Interpretation als MAP Schätzung eines binären Klassifikationsproblems hat. Das Modell nimmt letztlich die Form eines globalen Minimierungsproblems an, das mit herkömmlichen Optimierungsverfahren gelöst werden kann. Der konkrete Typ der verwendeten Bildmerkmale, Ähnlichkeitsmaße und räumlichen Beziehungen ist nicht explizit vorgeschrieben. Ein wichtiger Vorteil unseres Modells gegenüber vergleichbaren Verfahren ist seine Fähigkeit, Schwachpunkte einer Informationsquelle implizit durch die Stärken anderer Informationsquellen zu kompensieren. In unseren Experimenten konzentrieren wir uns insbesondere auf Bilder schwach texturierter Szenen als ein Beispiel schwieriger Zuordnungsprobleme. Die Anzahl stabiler Bildmerkmale ist hier typischerweise gering, und die Unterscheidbarkeit der Merkmalsbeschreibungen schlecht. Anhand des vorgeschlagenen Modells implementieren wir einen konkreten Wide Baseline Stereo Matching Algorithmus, der besser mit schwacher Textur umgehen kann als herkömmliche Verfahren. Um die praktische Relevanz zu verdeutlichen, wenden wir den Algorithmus für die automatische Bildorientierung an. Hier besteht die Aufgabe darin, zu einer Menge überlappender Bilder die relativen 3D Kamerapositionen und Kameraorientierungen zu bestimmen. Wir zeigen, dass der Algorithmus im Fall schwach texturierter Szenen bessere Ergebnisse als etablierte Verfahren ermöglicht, und dennoch bei Standard-Datensätzen vergleichbare Ergebnisse liefert

Contour Proposal Networks for Biomedical Instance Segmentation

We present a conceptually simple framework for object instance segmentation called Contour Proposal Network (CPN), which detects possibly overlapping objects in an image while simultaneously fitting closed object contours using an interpretable, fixed-sized representation based on Fourier Descriptors. The CPN can incorporate state of the art object detection architectures as backbone networks into a single-stage instance segmentation model that can be trained end-to-end. We construct CPN models with different backbone networks, and apply them to instance segmentation of cells in datasets from different modalities. In our experiments, we show CPNs that outperform U-Nets and Mask R-CNNs in instance segmentation accuracy, and present variants with execution times suitable for real-time applications. The trained models generalize well across different domains of cell types. Since the main assumption of the framework are closed object contours, it is applicable to a wide range of detection problems also outside the biomedical domain. An implementation of the model architecture in PyTorch is freely available

Contrastive Representation Learning for Whole Brain Cytoarchitectonic Mapping in Histological Human Brain Sections

Cytoarchitectonic maps provide microstructural reference parcellations of the brain, describing its organization in terms of the spatial arrangement of neuronal cell bodies as measured from histological tissue sections. Recent work provided the first automatic segmentations of cytoarchitectonic areas in the visual system using Convolutional Neural Networks. We aim to extend this approach to become applicable to a wider range of brain areas, envisioning a solution for mapping the complete human brain. Inspired by recent success in image classification, we propose a contrastive learning objective for encoding microscopic image patches into robust microstructural features, which are efficient for cytoarchitectonic area classification. We show that a model pre-trained using this learning task outperforms a model trained from scratch, as well as a model pre-trained on a recently proposed auxiliary task. We perform cluster analysis in the feature space to show that the learned representations form anatomically meaningful groups.Comment: Accepted to ISBI 202

Denoising Diffusion Probabilistic Models for Image Inpainting of Cell Distributions in the Human Brain

Recent advances in imaging and high-performance computing have made it possible to image the entire human brain at the cellular level. This is the basis to study the multi-scale architecture of the brain regarding its subdivision into brain areas and nuclei, cortical layers, columns, and cell clusters down to single cell morphology Methods for brain mapping and cell segmentation exploit such images to enable rapid and automated analysis of cytoarchitecture and cell distribution in complete series of histological sections. However, the presence of inevitable processing artifacts in the image data caused by missing sections, tears in the tissue, or staining variations remains the primary reason for gaps in the resulting image data. To this end we aim to provide a model that can fill in missing information in a reliable way, following the true cell distribution at different scales. Inspired by the recent success in image generation, we propose a denoising diffusion probabilistic model (DDPM), trained on light-microscopic scans of cell-body stained sections. We extend this model with the RePaint method to impute missing or replace corrupted image data. We show that our trained DDPM is able to generate highly realistic image information for this purpose, generating plausible cell statistics and cytoarchitectonic patterns. We validate its outputs using two established downstream task models trained on the same data.Comment: Submitted to ISBI-202

Improving Cytoarchitectonic Segmentation of Human Brain Areas with Self-supervised Siamese Networks

Cytoarchitectonic parcellations of the human brain serve as anatomical references in multimodal atlas frameworks. They are based on analysis of cell-body stained histological sections and the identification of borders between brain areas. The de-facto standard involves a semi-automatic, reproducible border detection, but does not scale with high-throughput imaging in large series of sections at microscopical resolution. Automatic parcellation, however, is extremely challenging due to high variation in the data, and the need for a large field of view at microscopic resolution. The performance of a recently proposed Convolutional Neural Network model that addresses this problem especially suffers from the naturally limited amount of expert annotations for training. To circumvent this limitation, we propose to pre-train neural networks on a self-supervised auxiliary task, predicting the 3D distance between two patches sampled from the same brain. Compared to a random initialization, fine-tuning from these networks results in significantly better segmentations. We show that the self-supervised model has implicitly learned to distinguish several cortical brain areas -- a strong indicator that the proposed auxiliary task is appropriate for cytoarchitectonic mapping.Comment: Accepted at MICCAI 201

Bringing Anatomical Information into Neuronal Network Models

For constructing neuronal network models computational neuroscientists have access to wide-ranging anatomical data that nevertheless tend to cover only a fraction of the parameters to be determined. Finding and interpreting the most relevant data, estimating missing values, and combining the data and estimates from various sources into a coherent whole is a daunting task. With this chapter we aim to provide guidance to modelers by describing the main types of anatomical data that may be useful for informing neuronal network models. We further discuss aspects of the underlying experimental techniques relevant to the interpretation of the data, list particularly comprehensive data sets, and describe methods for filling in the gaps in the experimental data. Such methods of `predictive connectomics' estimate connectivity where the data are lacking based on statistical relationships with known quantities. It is instructive, and in certain cases necessary, to use organizational principles that link the plethora of data within a unifying framework where regularities of brain structure can be exploited to inform computational models. In addition, we touch upon the most prominent features of brain organization that are likely to influence predicted neuronal network dynamics, with a focus on the mammalian cerebral cortex. Given the still existing need for modelers to navigate a complex data landscape full of holes and stumbling blocks, it is vital that the field of neuroanatomy is moving toward increasingly systematic data collection, representation, and publication