Machine Learning for Instance Segmentation

Volumetric Electron Microscopy images can be used for connectomics, the study of brain connectivity at the cellular level. A prerequisite for this inquiry is the automatic identification of neural cells, which requires machine learning algorithms and in particular efficient image segmentation algorithms. In this thesis, we develop new algorithms for this task. In the first part we provide, for the first time in this field, a method for training a neural network to predict optimal input data for a watershed algorithm. We demonstrate its superior performance compared to other segmentation methods of its category. In the second part, we develop an efficient watershed-based algorithm for weighted graph partitioning, the \emph{Mutex Watershed}, which uses negative edge-weights for the first time. We show that it is intimately related to the multicut and has a cutting edge performance on a connectomics challenge. Our algorithm is currently used by the leaders of two connectomics challenges. Finally, motivated by inpainting neural networks, we create a method to learn the graph weights without any supervision

A Generalized Framework for Agglomerative Clustering of Signed Graphs applied to Instance Segmentation

We propose a novel theoretical framework that generalizes algorithms for hierarchical agglomerative clustering to weighted graphs with both attractive and repulsive interactions between the nodes. This framework defines GASP, a Generalized Algorithm for Signed graph Partitioning, and allows us to explore many combinations of different linkage criteria and cannot-link constraints. We prove the equivalence of existing clustering methods to some of those combinations, and introduce new algorithms for combinations which have not been studied. An extensive comparison is performed to evaluate properties of the clustering algorithms in the context of instance segmentation in images, including robustness to noise and efficiency. We show how one of the new algorithms proposed in our framework outperforms all previously known agglomerative methods for signed graphs, both on the competitive CREMI 2016 EM segmentation benchmark and on the CityScapes dataset.Comment: 19 pages, 8 figures, 6 table

Learning Instance Segmentation from Sparse Supervision

Instance segmentation is an important task in many domains of automatic image processing, such as self-driving cars, robotics and microscopy data analysis. Recently, deep learning-based algorithms have brought image segmentation close to human performance. However, most existing models rely on dense groundtruth labels for training, which are expensive, time consuming and often require experienced annotators to perform the labeling. Besides the annotation burden, training complex high-capacity neural networks depends upon non-trivial expertise in the choice and tuning of hyperparameters, making the adoption of these models challenging for researchers in other fields. The aim of this work is twofold. The first is to make the deep learning segmentation methods accessible to non-specialist. The second is to address the dense annotation problem by developing instance segmentation methods trainable with limited groundtruth data. In the first part of this thesis, I bring state-of-the-art instance segmentation methods closer to non-experts by developing PlantSeg: a pipeline for volumetric segmentation of light microscopy images of biological tissues into cells. PlantSeg comes with a large repository of pre-trained models and delivers highly accurate results on a variety of samples and image modalities. We exemplify its usefulness to answer biological questions in several collaborative research projects. In the second part, I tackle the dense annotation bottleneck by introducing SPOCO, an instance segmentation method, which can be trained from just a few annotated objects. It demonstrates strong segmentation performance on challenging natural and biological benchmark datasets at a very reduced manual annotation cost and delivers state-of-the-art results on the CVPPP benchmark. In summary, my contributions enable training of instance segmentation models with limited amounts of labeled data and make these methods more accessible for non-experts, speeding up the process of quantitative data analysis

Segmentation and semantic labelling of RGBD data with convolutional neural networks and surface fitting

We present an approach for segmentation and semantic labelling of RGBD data exploiting together geometrical cues and deep learning techniques. An initial over-segmentation is performed using spectral clustering and a set of non-uniform rational B-spline surfaces is fitted on the extracted segments. Then a convolutional neural network (CNN) receives in input colour and geometry data together with surface fitting parameters. The network is made of nine convolutional stages followed by a softmax classifier and produces a vector of descriptors for each sample. In the next step, an iterative merging algorithm recombines the output of the over-segmentation into larger regions matching the various elements of the scene. The couples of adjacent segments with higher similarity according to the CNN features are candidate to be merged and the surface fitting accuracy is used to detect which couples of segments belong to the same surface. Finally, a set of labelled segments is obtained by combining the segmentation output with the descriptors from the CNN. Experimental results show how the proposed approach outperforms state-of-the-art methods and provides an accurate segmentation and labelling

Designing Deep Learning Frameworks for Plant Biology

In recent years the parallel progress in high-throughput microscopy and deep learning drastically widened the landscape of possible research avenues in life sciences. In particular, combining high-resolution microscopic images and automated imaging pipelines powered by deep learning dramatically reduced the manual annotation work required for quantitative analysis. In this work, we will present two deep learning frameworks tailored to the needs of life scientists in the context of plant biology. First, we will introduce PlantSeg, a software for 2D and 3D instance segmentation. The PlantSeg pipeline contains several pre-trained models for different microscopy modalities and multiple popular graph-based instance segmentation algorithms. In the second part, we will present CellTypeGraph, a benchmark for quantitatively evaluating graph neural networks. The benchmark is designed to test the ability of machine learning methods to classify the types of cells in an \textit{Arabidopsis thaliana} ovules. CellTypeGraph's prime aim is to give a valuable tool to the geometric learning community, but at the same time it also offers a framework for plant biologists to perform fast and accurate cell type inference on new data

Stateless actor-critic for instance segmentation with high-level priors

Instance segmentation is an important computer vision problem which remains challenging despite impressive recent advances due to deep learning-based methods. Given sufficient training data, fully supervised methods can yield excellent performance, but annotation of ground-truth data remains a major bottleneck, especially for biomedical applications where it has to be performed by domain experts. The amount of labels required can be drastically reduced by using rules derived from prior knowledge to guide the segmentation. However, these rules are in general not differentiable and thus cannot be used with existing methods. Here, we relax this requirement by using stateless actor critic reinforcement learning, which enables non-differentiable rewards. We formulate the instance segmentation problem as graph partitioning and the actor critic predicts the edge weights driven by the rewards, which are based on the conformity of segmented instances to high-level priors on object shape, position or size. The experiments on toy and real datasets demonstrate that we can achieve excellent performance without any direct supervision based only on a rich set of priors