Background: Fluorescence microscopy is widely used to determine the subcellular location of proteins. Efforts to determine location on a proteome-wide basis create a need for automated methods to analyze the resulting images. Over the past ten years, the feasibility of using machine learning methods to recognize all major subcellular location patterns has been convincingly demonstrated, using diverse feature sets and classifiers. On a well-studied data set of 2D HeLa single-cell images, the best performance to date, 91.5%, was obtained by including a set of multiresolution features. This demonstrates the value of multiresolution approaches to this important problem.

We propose an algorithm for adaptive efficient acquisition of fluorescence microscopy data sets using a multirate (MR) approach. We simulate acquisition as part of a larger system for protein classification based on their subcellular location patterns and, thus, strive to maintain the achieved level of classification accuracy as much as possible. This problem is similar to image compression but unique due to additional restrictions, namely causality; we have access only to the information scanned up to that point. While we do want to acquire fewer samples with as low distortion as possible to achieve compression, our goal is to do so while affecting the overall classification accuracy as little as possible. We achieve this by using an adaptive MR scanning scheme which samples the regions of the image area that hold the most pertinent information. Our results show that we can achieve significant compression which we can then use to aquire faster or to increase space resolution of our data set, all while minimally affecting the classification accuracy of the entire system.

We propose an algorithm for the classification of fluorescence microscopy images depicting the spatial distribution of proteins within the cell. The problem is at the forefront of the current trend in biology towards understanding the role and function of all proteins. The importance of protein subcellular location was pointed out by Murphy, whose group produced the first automated system for classification of images depicting these locations, based on diverse feature sets and combinations of classifiers. With the addition of the simplest multiresolution features, the same group obtained the highest reported accuracy of 91.5% for the denoised 2D HeLa data set. Here, we aim to improve upon that system by adding the true power of multiresolution-adaptivity. In the process, we build a system able to work with any feature sets and any classifiers, which we denote as a Generic Classification System (GCS). Our system consists of multiresolution (MR) decomposition in the front, followed by feature computation and classification in each subband, yielding local decisions. This is followed by the crucial step of combining all those local decisions into a global one, while at the same time ensuring that the resulting system does no worse than a no-decomposition one. On a nondenoised data set and a much smaller number of features (a combination of texture and Zernicke moment features) and a neural network classifier, we obtain a high accuracy of 89.8%, effectively proving that the space-frequency localized information in the subbands adds to the discriminative power of the system.

We propose an adaptive multiresolution (MR) approach for classification of fluorescence microscopy images of subcellular protein locations, providing biologically relevant information. These images have highly localized features both in space and frequency which naturally leads us to MR tools. Moreover, as the goal of the classification system is to distinguish between various protein classes, we aim for features adapted to individual proteins. These two requirements further lead us to adaptive MR tools. We start with a simple classification system consisting of Haralick texture feature computation followed by a maximum-likelihood classifier, and demonstrate that, by adding an MR block in front, we are able to raise the average classification accuracy by roughly 10%. We conclude that selecting features in MR subspaces allows us to custom-build discriminative feature sets for fluorescence microscopy images of protein subcellular location images.

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