A high-density scalp EEG dataset acquired during brief naps after a visual working memory task.

There is growing interest in understanding how specific neural events that occur during sleep, including characteristic spindle oscillations between 10 and 16 Hz (Hz), are related to learning and memory. Neural events can be recorded during sleep using the well-known method of scalp electroencephalography (EEG). While publicly available sleep EEG datasets exist, most consist of only a few channels collected in specific patient groups being evaluated overnight for sleep disorders in clinical settings. The dataset described in this Data in Brief includes 22 participants who each participated in EEG recordings on two separate days. The dataset includes manual annotation of sleep stages and 2528 manually annotated spindles. Signals from 64-channels were continuously recorded at 1 kHz with a high-density active electrode system while participants napped for 30 or 60 min inside a sound-attenuated testing booth after performing a high- or low-load visual working memory task where load was randomized across recording days. The high-density EEG datasets present several advantages over single- or few-channel datasets including most notably the opportunity to explore spatial differences in the distribution of neural events, including whether spindles occur locally on only a few channels or co-occur globally across many channels, whether spindle frequency, duration, and amplitude vary as a function of brain hemisphere and anterior-posterior axis, and whether the probability of spindle occurrence varies as a function of the phase of ongoing slow oscillations. The dataset, along with python source code for file input and signal processing, is made freely available at the Open Science Framework through the link https://osf.io/chav7/.

Identifying sleep spindles with multichannel EEG and classification optimization.

Researchers classify critical neural events during sleep called spindles that are related to memory consolidation using the method of scalp electroencephalography (EEG). Manual classification is time consuming and is susceptible to low inter-rater agreement. This could be improved using an automated approach. This study presents an optimized filter based and thresholding (FBT) model to set up a baseline for comparison to evaluate machine learning models using naïve features, such as raw signals, peak frequency, and dominant power. The FBT model allows us to formally define sleep spindles using signal processing but may miss examples most human scorers would agree are spindles. Machine learning methods in theory should be able to approach performance of human raters but they require a large quantity of scored data, proper feature representation, intensive feature engineering, and model selection. We evaluate both the FBT model and machine learning models with naïve features. We show that the machine learning models derived from the FBT model improve classification performance. An automated approach designed for the current data was applied to the DREAMS dataset [1]. With one of the expert's annotation as a gold standard, our pipeline yields an excellent sensitivity that is close to a second expert's scores and with the advantage that it can classify spindles based on multiple channels if more channels are available. More importantly, our pipeline could be modified as a guide to aid manual annotation of sleep spindles based on multiple channels quickly (6-10 s for processing a 40-min EEG recording), making spindle detection faster and more objective.

Interactive semiautomatic contour delineation using statistical conditional random fields framework.

PURPOSE: Contouring a normal anatomical structure during radiation treatment planning requires significant time and effort. The authors present a fast and accurate semiautomatic contour delineation method to reduce the time and effort required of expert users. METHODS: Following an initial segmentation on one CT slice, the user marks the target organ and nontarget pixels with a few simple brush strokes. The algorithm calculates statistics from this information that, in turn, determines the parameters of an energy function containing both boundary and regional components. The method uses a conditional random field graphical model to define the energy function to be minimized for obtaining an estimated optimal segmentation, and a graph partition algorithm to efficiently solve the energy function minimization. Organ boundary statistics are estimated from the segmentation and propagated to subsequent images; regional statistics are estimated from the simple brush strokes that are either propagated or redrawn as needed on subsequent images. This greatly reduces the user input needed and speeds up segmentations. The proposed method can be further accelerated with graph-based interpolation of alternating slices in place of user-guided segmentation. CT images from phantom and patients were used to evaluate this method. The authors determined the sensitivity and specificity of organ segmentations using physician-drawn contours as ground truth, as well as the predicted-to-ground truth surface distances. Finally, three physicians evaluated the contours for subjective acceptability. Interobserver and intraobserver analysis was also performed and Bland-Altman plots were used to evaluate agreement. RESULTS: Liver and kidney segmentations in patient volumetric CT images show that boundary samples provided on a single CT slice can be reused through the entire 3D stack of images to obtain accurate segmentation. In liver, our method has better sensitivity and specificity (0.925 and 0.995) than region growing (0.897 and 0.995) and level set methods (0.912 and 0.985) as well as shorter mean predicted-to-ground truth distance (2.13 mm) compared to regional growing (4.58 mm) and level set methods (8.55 mm and 4.74 mm). Similar results are observed in kidney segmentation. Physician evaluation of ten liver cases showed that 83% of contours did not need any modification, while 6% of contours needed modifications as assessed by two or more evaluators. In interobserver and intraobserver analysis, Bland-Altman plots showed our method to have better repeatability than the manual method while the delineation time was 15% faster on average. CONCLUSIONS: Our method achieves high accuracy in liver and kidney segmentation and considerably reduces the time and labor required for contour delineation. Since it extracts purely statistical information from the samples interactively specified by expert users, the method avoids heuristic assumptions commonly used by other methods. In addition, the method can be expanded to 3D directly without modification because the underlying graphical framework and graph partition optimization method fit naturally with the image grid structure.

Semi-automatic medical image segmentation with adaptive local statistics in Conditional Random Fields framework.

Planning radiotherapy and surgical procedures usually require onerous manual segmentation of anatomical structures from medical images. In this paper we present a semi-automatic and accurate segmentation method to dramatically reduce the time and effort required of expert users. This is accomplished by giving a user an intuitive graphical interface to indicate samples of target and non-target tissue by loosely drawing a few brush strokes on the image. We use these brush strokes to provide the statistical input for a Conditional Random Field (CRF) based segmentation. Since we extract purely statistical information from the user input, we eliminate the need of assumptions on boundary contrast previously used by many other methods, A new feature of our method is that the statistics on one image can be reused on related images without registration. To demonstrate this, we show that boundary statistics provided on a few 2D slices of volumetric medical data, can be propagated through the entire 3D stack of images without using the geometric correspondence between images. In addition, the image segmentation from the CRF can be formulated as a minimum s-t graph cut problem which has a solution that is both globally optimal and fast. The combination of a fast segmentation and minimal user input that is reusable, make this a powerful technique for the segmentation of medical images.

Multiresolution histograms and their use for recognition.

The histogram of image intensities is used extensively for recognition and for retrieval of images and video from visual databases. A single image histogram, however, suffers from the inability to encode spatial image variation. An obvious way to extend this feature is to compute the histograms of multiple resolutions of an image to form a multiresolution histogram. The multiresolution histogram shares many desirable properties with the plain histogram including that they are both fast to compute, space efficient, invariant to rigid motions, and robust to noise. In addition, the multiresolution histogram directly encodes spatial information. We describe a simple yet novel matching algorithm based on the multiresolution histogram that uses the differences between histograms of consecutive image resolutions. We evaluate it against five widely used image features. We show that with our simple feature we achieve or exceed the performance obtained with more complicated features. Further, we show our algorithm to be the most efficient and robust.

Modeling the space of camera response functions.

Many vision applications require precise measurement of scene radiance. The function relating scene radiance to image intensity of an imaging system is called the camera response. We analyze the properties that all camera responses share. This allows us to find the constraints that any response function must satisfy. These constraints determine the theoretical space of all possible camera responses. We have collected a diverse database of real-world camera response functions (DoRF). Using this database, we show that real-world responses occupy a small part of the theoretical space of all possible responses. We combine the constraints from our theoretical space with the data from DoRF to create a low-parameter empirical model of response (EMoR). This response model allows us to accurately interpolate the complete response function of a camera from a small number of measurements obtained using a standard chart. We also show that the model can be used to accurately estimate the camera response from images of an arbitrary scene taken using different exposures. The DoRF database and the EMoR model can be downloaded at http://www.cs.columbia.edu/CAVE.