Automatic Segmentation of Fluorescence Lifetime Microscopy Images of Cells Using Multi-Resolution Community Detection

We have developed an automatic method for segmenting fluorescence lifetime (FLT) imaging microscopy (FLIM) images of cells inspired by a multi-resolution community detection (MCD) based network segmentation method. The image processing problem is framed as identifying segments with respective average FLTs against a background in FLIM images. The proposed method segments a FLIM image for a given resolution of the network composed using image pixels as the nodes and similarity between the pixels as the edges. In the resulting segmentation, low network resolution leads to larger segments and high network resolution leads to smaller segments. Further, the mean-square error (MSE) in estimating the FLT segments in a FLIM image using the proposed method was found to be consistently decreasing with increasing resolution of the corresponding network. The proposed MCD method outperformed a popular spectral clustering based method in performing FLIM image segmentation. The spectral segmentation method introduced noisy segments in its output at high resolution. It was unable to offer a consistent decrease in MSE with increasing resolution.Comment: 21 pages, 6 figure

Superpixels: An Evaluation of the State-of-the-Art

Superpixels group perceptually similar pixels to create visually meaningful entities while heavily reducing the number of primitives for subsequent processing steps. As of these properties, superpixel algorithms have received much attention since their naming in 2003. By today, publicly available superpixel algorithms have turned into standard tools in low-level vision. As such, and due to their quick adoption in a wide range of applications, appropriate benchmarks are crucial for algorithm selection and comparison. Until now, the rapidly growing number of algorithms as well as varying experimental setups hindered the development of a unifying benchmark. We present a comprehensive evaluation of 28 state-of-the-art superpixel algorithms utilizing a benchmark focussing on fair comparison and designed to provide new insights relevant for applications. To this end, we explicitly discuss parameter optimization and the importance of strictly enforcing connectivity. Furthermore, by extending well-known metrics, we are able to summarize algorithm performance independent of the number of generated superpixels, thereby overcoming a major limitation of available benchmarks. Furthermore, we discuss runtime, robustness against noise, blur and affine transformations, implementation details as well as aspects of visual quality. Finally, we present an overall ranking of superpixel algorithms which redefines the state-of-the-art and enables researchers to easily select appropriate algorithms and the corresponding implementations which themselves are made publicly available as part of our benchmark at davidstutz.de/projects/superpixel-benchmark/

Location Dependent Dirichlet Processes

Dirichlet processes (DP) are widely applied in Bayesian nonparametric modeling. However, in their basic form they do not directly integrate dependency information among data arising from space and time. In this paper, we propose location dependent Dirichlet processes (LDDP) which incorporate nonparametric Gaussian processes in the DP modeling framework to model such dependencies. We develop the LDDP in the context of mixture modeling, and develop a mean field variational inference algorithm for this mixture model. The effectiveness of the proposed modeling framework is shown on an image segmentation task

Deep clustering: Discriminative embeddings for segmentation and separation

We address the problem of acoustic source separation in a deep learning framework we call "deep clustering." Rather than directly estimating signals or masking functions, we train a deep network to produce spectrogram embeddings that are discriminative for partition labels given in training data. Previous deep network approaches provide great advantages in terms of learning power and speed, but previously it has been unclear how to use them to separate signals in a class-independent way. In contrast, spectral clustering approaches are flexible with respect to the classes and number of items to be segmented, but it has been unclear how to leverage the learning power and speed of deep networks. To obtain the best of both worlds, we use an objective function that to train embeddings that yield a low-rank approximation to an ideal pairwise affinity matrix, in a class-independent way. This avoids the high cost of spectral factorization and instead produces compact clusters that are amenable to simple clustering methods. The segmentations are therefore implicitly encoded in the embeddings, and can be "decoded" by clustering. Preliminary experiments show that the proposed method can separate speech: when trained on spectrogram features containing mixtures of two speakers, and tested on mixtures of a held-out set of speakers, it can infer masking functions that improve signal quality by around 6dB. We show that the model can generalize to three-speaker mixtures despite training only on two-speaker mixtures. The framework can be used without class labels, and therefore has the potential to be trained on a diverse set of sound types, and to generalize to novel sources. We hope that future work will lead to segmentation of arbitrary sounds, with extensions to microphone array methods as well as image segmentation and other domains.Comment: Originally submitted on June 5, 201