Reconstruction of the cell pseudo-space from single-cell RNA sequencing data with scSpace.

Tissues are highly complicated with spatial heterogeneity in gene expression. However, the cutting-edge single-cell RNA-seq technology eliminates the spatial information of individual cells, which contributes to the characterization of cell identities. Herein, we propose single-cell spatial position associated co-embeddings (scSpace), an integrative method to identify spatially variable cell subpopulations by reconstructing cells onto a pseudo-space with spatial transcriptome references (Visium, STARmap, Slide-seq, etc.). We benchmark scSpace with both simulated and biological datasets, and demonstrate that scSpace can accurately and robustly identify spatially variated cell subpopulations. When employed to reconstruct the spatial architectures of complex tissue such as the brain cortex, the small intestinal villus, the liver lobule, the kidney, the embryonic heart, and others, scSpace shows promising performance on revealing the pairwise cellular spatial association within single-cell data. The application of scSpace in melanoma and COVID-19 exhibits a broad prospect in the discovery of spatial therapeutic markers.

De novo analysis of bulk RNA-seq data at spatially resolved single-cell resolution.

Uncovering the tissue molecular architecture at single-cell resolution could help better understand organisms' biological and pathological processes. However, bulk RNA-seq can only measure gene expression in cell mixtures, without revealing the transcriptional heterogeneity and spatial patterns of single cells. Herein, we introduce Bulk2Space ( https://github.com/ZJUFanLab/bulk2space ), a deep learning framework-based spatial deconvolution algorithm that can simultaneously disclose the spatial and cellular heterogeneity of bulk RNA-seq data using existing single-cell and spatial transcriptomics references. The use of bulk transcriptomics to validate Bulk2Space unveils, in particular, the spatial variance of immune cells in different tumor regions, the molecular and spatial heterogeneity of tissues during inflammation-induced tumorigenesis, and spatial patterns of novel genes in different cell types. Moreover, Bulk2Space is utilized to perform spatial deconvolution analysis on bulk transcriptome data from two different mouse brain regions derived from our in-house developed sequencing approach termed Spatial-seq. We have not only reconstructed the hierarchical structure of the mouse isocortex but also further annotated cell types that were not identified by original methods in the mouse hypothalamus.

Improving Low-dose Cardiac CT Images based on 3D Sparse Representation.

Cardiac computed tomography (CCT) is a reliable and accurate tool for diagnosis of coronary artery diseases and is also frequently used in surgery guidance. Low-dose scans should be considered in order to alleviate the harm to patients caused by X-ray radiation. However, low dose CT (LDCT) images tend to be degraded by quantum noise and streak artifacts. In order to improve the cardiac LDCT image quality, a 3D sparse representation-based processing (3D SR) is proposed by exploiting the sparsity and regularity of 3D anatomical features in CCT. The proposed method was evaluated by a clinical study of 14 patients. The performance of the proposed method was compared to the 2D spares representation-based processing (2D SR) and the state-of-the-art noise reduction algorithm BM4D. The visual assessment, quantitative assessment and qualitative assessment results show that the proposed approach can lead to effective noise/artifact suppression and detail preservation. Compared to the other two tested methods, 3D SR method can obtain results with image quality most close to the reference standard dose CT (SDCT) images.

Radiation dose reduction with dictionary learning based processing for head CT.

In CT, ionizing radiation exposure from the scan has attracted much concern from patients and doctors. This work is aimed at improving head CT images from low-dose scans by using a fast Dictionary learning (DL) based post-processing. Both Low-dose CT (LDCT) and Standard-dose CT (SDCT) nonenhanced head images were acquired in head examination from a multi-detector row Siemens Somatom Sensation 16 CT scanner. One hundred patients were involved in the experiments. Two groups of LDCT images were acquired with 50 % (LDCT50 %) and 25 % (LDCT25 %) tube current setting in SDCT. To give quantitative evaluation, Signal to noise ratio (SNR) and Contrast to noise ratio (CNR) were computed from the Hounsfield unit (HU) measurements of GM, WM and CSF tissues. A blinded qualitative analysis was also performed to assess the processed LDCT datasets. Fifty and seventy five percent dose reductions are obtained for the two LDCT groups (LDCT50 %, 1.15 ± 0.1 mSv; LDCT25 %, 0.58 ± 0.1 mSv; SDCT, 2.32 ± 0.1 mSv; P < 0.001). Significant SNR increase over the original LDCT images is observed in the processed LDCT images for all the GM, WM and CSF tissues. Significant GM-WM CNR enhancement is noted in the DL processed LDCT images. Higher SNR and CNR than the reference SDCT images can even be achieved in the processed LDCT50 % and LDCT25 % images. Blinded qualitative review validates the perceptual improvements brought by the proposed approach. Compared to the original LDCT images, the application of DL processing in head CT is associated with a significant improvement of image quality.