Maximum a posteriori spatial probability segmen

An image segmentation algorithm that performs pixel-by-pixel segmentation on an image with consideration of the spatial information is described. The spatial information is the joint grey level values of the pixel to be segmented and its neighbouring pixels. The conditional probability that a pixel belongs to a particular class under the condition that the spatial information has been observed is defined to be the a posteriori spatial probability. A maximum a posteriori spatial probability (MASP) segmentation algorithm is proposed to segment an image such that each pixel is segmented into a particular class when the a posteriori spatial probability is a maximum. The proposed segmentation algorithm is implemented in an iterative form. During the iteration, a series of intermediate segmented images are produced among which the one that possesses the maximum amount of information in its spatial structure is chosen as the optimum segmented image. Results from segmenting synthetic and practical images demonstrate that the MASP algorithm is capable of achieving better results when compared with other global thresholding methods.published_or_final_versio

An iterative image segmentation algorithm utilizing spatial information

An iterative image segmentation algorithm that segments an image on a pixel-by-pixel basis is described. The observation information to be utilized is the joint gray level values of the pixel to be segmented and those of its neighborhood pixels. The iterative process is initialized by thresholding the image with Otsu's (1979) method. Each pixel is segmented into a class when the a posteriori probability, conditioned on the observation information, that it belongs to this class is a maximum. The newly segmented image is employed to re-estimate the a posteriori probabilities and the segmentation process is repeated until there is no further pixel classification change in a particular run. Among those segmented images generated in the iterative process, the best segmented image is chosen, according to a maximum entropy criterion. Simulation studies demonstrate that the proposed algorithm can achieve very significant improvement in segmentation performance as compared to the more popular thresholds approach. Furthermore, the performance is neither sensitive to the initial threshold value nor the form of the probability density function of the image. Segmentation of practical images also demonstrates that the proposed algorithm is capable of good segmentation results for real-life images.published_or_final_versio

Automatic cell segmentation by adaptive thresholding (ACSAT) for large-scale calcium imaging datasets

Advances in calcium imaging have made it possible to record from an increasingly larger number of neurons simultaneously. Neuroscientists can now routinely image hundreds to thousands of individual neurons. An emerging technical challenge that parallels the advancement in imaging a large number of individual neurons is the processing of correspondingly large datasets. One important step is the identification of individual neurons. Traditional methods rely mainly on manual or semimanual inspection, which cannot be scaled for processing large datasets. To address this challenge, we focused on developing an automated segmentation method, which we refer to as automated cell segmentation by adaptive thresholding (ACSAT). ACSAT works with a time-collapsed image and includes an iterative procedure that automatically calculates global and local threshold values during successive iterations based on the distribution of image pixel intensities. Thus, the algorithm is capable of handling variations in morphological details and in fluorescence intensities in different calcium imaging datasets. In this paper, we demonstrate the utility of ACSAT by testing it on 500 simulated datasets, two wide-field hippocampus datasets, a wide-field striatum dataset, a wide-field cell culture dataset, and a two-photon hippocampus dataset. For the simulated datasets with truth, ACSAT achieved >80% recall and precision when the signal-to-noise ratio was no less than ∼24 dB.DP2 NS082126 - NINDS NIH HHSPublished versio

Accurate detection of dysmorphic nuclei using dynamic programming and supervised classification

A vast array of pathologies is typified by the presence of nuclei with an abnormal morphology. Dysmorphic nuclear phenotypes feature dramatic size changes or foldings, but also entail much subtler deviations such as nuclear protrusions called blebs. Due to their unpredictable size, shape and intensity, dysmorphic nuclei are often not accurately detected in standard image analysis routines. To enable accurate detection of dysmorphic nuclei in confocal and widefield fluorescence microscopy images, we have developed an automated segmentation algorithm, called Blebbed Nuclei Detector (BleND), which relies on two-pass thresholding for initial nuclear contour detection, and an optimal path finding algorithm, based on dynamic programming, for refining these contours. Using a robust error metric, we show that our method matches manual segmentation in terms of precision and outperforms state-of-the-art nuclear segmentation methods. Its high performance allowed for building and integrating a robust classifier that recognizes dysmorphic nuclei with an accuracy above 95%. The combined segmentation-classification routine is bound to facilitate nucleus-based diagnostics and enable real-time recognition of dysmorphic nuclei in intelligent microscopy workflows