Calcium imaging is an important technique for monitoring the activity of thousands of neurons simultaneously. As calcium imaging datasets grow in size, automated detection of individual neurons is becoming important. Here we apply a supervised learning approach to this problem and show that convolutional networks can achieve near-human accuracy and superhuman speed. Accuracy is superior to the popular PCA/ICA method based on precision and recall relative to ground truth annotation by a human expert. These results suggest that convolutional networks are an efficient and flexible tool for the analysis of large-scale calcium imaging data.

Objective: To propose and validate an unsupervised MRI reconstruction method that does not require fully sampled k-space data. Materials and Methods: The proposed method, deep image prior with structured sparsity (DISCUS), extends the deep image prior (DIP) by introducing group sparsity to frame-specific code vectors, enabling the discovery of a low-dimensional manifold for capturing temporal variations. \discus was validated using four studies: (I) simulation of a dynamic Shepp-Logan phantom to demonstrate its manifold discovery capabilities, (II) comparison with compressed sensing and DIP-based methods using simulated single-shot late gadolinium enhancement (LGE) image series from six distinct digital cardiac phantoms in terms of normalized mean square error (NMSE) and structural similarity index measure (SSIM), (III) evaluation on retrospectively undersampled single-shot LGE data from eight patients, and (IV) evaluation on prospectively undersampled single-shot LGE data from eight patients, assessed via blind scoring from two expert readers. Results: DISCUS outperformed competing methods, demonstrating superior reconstruction quality in terms of NMSE and SSIM (Studies I--III) and expert reader scoring (Study IV). Discussion: An unsupervised image reconstruction method is presented and validated on simulated and measured data. These developments can benefit applications where acquiring fully sampled data is challenging.

During and after a course of therapy, imaging is routinely used to monitor the disease progression and assess the treatment responses. Despite of its significance, reliably capturing and predicting the spatial-temporal anatomic changes from a sequence of patient-specific image series presents a considerable challenge. Thus, the development of a computational framework becomes highly desirable for a multitude of practical applications. In this context, we propose a strategy of Spatial-Temporal Neural Representation learning with Prior embedding (ST-NeRP) for patient-specific imaging study. Our strategy involves leveraging an Implicit Neural Representation (INR) network to encode the image at the reference time point into a prior embedding. Subsequently, a spatial-temporally continuous deformation function is learned through another INR network. This network is trained using the whole patient-specific image sequence, enabling the prediction of deformation fields at various target time points. The efficacy of the ST-NeRP model is demonstrated through its application to diverse sequential image series, including 4D CT and longitudinal CT datasets within thoracic and abdominal imaging. The proposed ST-NeRP model exhibits substantial potential in enabling the monitoring of anatomical changes within a patient throughout the therapeutic journey.

Background. Fully automatic analysis of myocardial perfusion MRI datasets enables rapid and objective reporting of stress/rest studies in patients with suspected ischemic heart disease. Developing deep learning techniques that can analyze multi-center datasets despite limited training data and variations in software and hardware is an ongoing challenge. Methods. Datasets from 3 medical centers acquired at 3T (n = 150 subjects) were included: an internal dataset (inD; n = 95) and two external datasets (exDs; n = 55) used for evaluating the robustness of the trained deep neural network (DNN) models against differences in pulse sequence (exD-1) and scanner vendor (exD-2). A subset of inD (n = 85) was used for training/validation of a pool of DNNs for segmentation, all using the same spatiotemporal U-Net architecture and hyperparameters but with different parameter initializations. We employed a space-time sliding-patch analysis approach that automatically yields a pixel-wise "uncertainty map" as a byproduct of the segmentation process. In our approach, a given test case is segmented by all members of the DNN pool and the resulting uncertainty maps are leveraged to automatically select the "best" one among the pool of solutions. Results. The proposed DAUGS analysis approach performed similarly to the established approach on the internal dataset (p = n.s.) whereas it significantly outperformed on the external datasets (p < 0.005 for exD-1 and exD-2). Moreover, the number of image series with "failed" segmentation was significantly lower for the proposed vs. the established approach (4.3% vs. 17.1%, p < 0.0005). Conclusions. The proposed DAUGS analysis approach has the potential to improve the robustness of deep learning methods for segmentation of multi-center stress perfusion datasets with variations in the choice of pulse sequence, site location or scanner vendor.

This data curation work introduces the first large-scale dataset of radial k-space and DICOM data for breast DCE-MRI acquired in diagnostic breast MRI exams. Our dataset includes case-level labels indicating patient age, menopause status, lesion status (negative, benign, and malignant), and lesion type for each case. The public availability of this dataset and accompanying reconstruction code will support research and development of fast and quantitative breast image reconstruction and machine learning methods.

Calcium imaging is an important technique for monitoring the activity of thousands of neurons simultaneously. As calcium imaging datasets grow in size, automated detection of individual neurons is becoming important. Here we apply a supervised learning approach to this problem and show that convolutional networks can achieve near-human accuracy and superhuman speed. Accuracy is superior to the popular PCA/ICA method based on precision and recall relative to ground truth annotation by a human expert. These results suggest that convolutional networks are an efficient and flexible tool for the analysis of large-scale calcium imaging data.

Maintaining farm sustainability through optimizing the agricultural management practices helps build more planet-friendly environment. The emerging satellite missions can acquire multi- and hyperspectral imagery which captures more detailed spectral information concerning the scanned area, hence allows us to benefit from subtle spectral features during the analysis process in agricultural applications. We introduce an approach for extracting 2.5 m cultivated land maps from 10 m Sentinel-2 multispectral image series which benefits from a compact graph convolutional neural network. The experiments indicate that our models not only outperform classical and deep machine learning techniques through delivering higher-quality segmentation maps, but also dramatically reduce the memory footprint when compared to U-Nets (almost 8k trainable parameters of our models, with up to 31M parameters of U-Nets). Such memory frugality is pivotal in the missions which allow us to uplink a model to the AI-powered satellite once it is in orbit, as sending large nets is impossible due to the time constraints.

Published under a CC BY 4.0 license. Supplemental material is available for this article. This dataset provides vertebral segmentation masks for spine CT images and annotations of vertebral fractures or abnormalities per vertebral level; it is available from https://osf.io/nqjyw/ This public CT dataset holds 160 image series of 141 patients including segmentation masks of 1725 fully visualized vertebrae; it is split into a training dataset (80 image series, 862 vertebrae), a public validation dataset (40 image series, 434 vertebrae), and a secret test dataset (40 image series, 429 vertebrae, to be released in December 2020). Metadata include annotations of vertebral fractures using the semiquantitative method by Genant and of instances of foreign material per vertebral level, as well as opportunistic measurements of lumbar bone mineral density per patient.

Purpose: To construct a neural network model that can learn the different diagnosing strategies of radiologists to better classify aneurysm status in magnetic resonance angiography images. Materials and methods: This retrospective study included 3423 time-of-flight brain magnetic resonance angiography image series (subjects: male 1843 [mean age, 50.2 +/- 11.7 years], female 1580 [50.8 +/- 11.3 years]) recorded from November 2017 through January 2019. The image series were read independently for aneurysm status by one of four board-certified radiologists, who were assisted by an established deep learning-based computer-assisted diagnosis (CAD) system. The constructed neural networks were trained to classify the aneurysm status of zero to five aneurysm-suspicious areas suggested by the CAD system for each image series, and any additional aneurysm areas added by the radiologists, and this classification was compared with the judgment of the annotating radiologist. Image series were randomly allocated to training and testing data in an 8:2 ratio. The accuracy of the classification was compared by receiver operating characteristic analysis between the control model that accepted only image data as input and the proposed model that additionally accepted the information of who the annotating radiologist was. The DeLong test was used to compare areas under the curves (P < 0.05 was considered significant). Results: The area under the curve was larger in the proposed model (0.845) than in the control model (0.793), and the difference was significant (P < 0.0001). Conclusion: The proposed model improved classification accuracy by learning the diagnosis strategies of individual annotating radiologists.

Archiving large sets of medical or cell images in digital libraries may require ordering randomly scattered sets of image data according to specific criteria, such as the spatial extent of a specific local color or contrast content that reveals different meaningful states of a physiological structure, tissue, or cell in a certain order, indicating progression or recession of a pathology, or the progressive response of a cell structure to treatment. Here we used a Self Organized Map (SOM)-based, fully automatic and unsupervised, classification procedure described in our earlier work and applied it to sets of minimally processed grayscale and/or color processed Scanning Electron Microscopy (SEM) images of CD4+ T-lymphocytes (so-called helper cells) with varying extent of HIV virion infection. It is shown that the quantization error in the SOM output after training permits to scale the spatial magnitude and the direction of change (+ or -) in local pixel contrast or color across images of a series with a reliability that exceeds that of any human expert. The procedure is easily implemented and fast, and represents a promising step towards low-cost automatic digital image archiving with minimal intervention of a human operator.