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Compressed sensing for highly efficient imaging transcriptomics.

ABSTRACT: Recent methods for spatial imaging of tissue samples can identify up to ~100 individual proteins^1-3 or RNAs^4-10 at single-cell resolution. However, the number of proteins or genes that can be studied in these approaches is limited by long imaging times. Here we introduce Composite In Situ Imaging (CISI), a method that leverages structure in gene expression across both cells and tissues to limit the number of imaging cycles needed to obtain spatially resolved gene expression maps. CISI defines gene modules that can be detected using composite measurements from imaging probes for subsets of genes. The data are then decompressed to recover expression values for individual genes. CISI further reduces imaging time by not relying on spot-level resolution, enabling lower magnification acquisition, and is overall about 500-fold more efficient than current methods. Applying CISI to 12 mouse brain sections, we accurately recovered the spatial abundance of 37 individual genes from 11 composite measurements covering 180 mm² and 476,276 cells.

SUBMITTER: Cleary B

PROVIDER: S-EPMC8355028 | biostudies-literature | 2021 Aug

REPOSITORIES: biostudies-literature

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Compressed sensing for highly efficient imaging transcriptomics.

Cleary Brian B Simonton Brooke B Bezney Jon J Murray Evan E Alam Shahul S Sinha Anubhav A Habibi Ehsan E Marshall Jamie J Lander Eric S ES Chen Fei F Regev Aviv A

Nature biotechnology 20210415 8

Recent methods for spatial imaging of tissue samples can identify up to ~100 individual proteins<sup>1-3</sup> or RNAs<sup>4-10</sup> at single-cell resolution. However, the number of proteins or genes that can be studied in these approaches is limited by long imaging times. Here we introduce Composite In Situ Imaging (CISI), a method that leverages structure in gene expression across both cells and tissues to limit the number of imaging cycles needed to obtain spatially resolved gene expression ...[more]

PMID: 33859401

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Project description:PurposeTo develop a method that combines parallel imaging and compressed sensing to enable faster and/or higher spatial resolution magnetic resonance (MR) imaging and show its feasibility in a pediatric clinical setting.Materials and methodsInstitutional review board approval was obtained for this HIPAA-compliant study, and informed consent or assent was given by subjects. A pseudorandom k-space undersampling pattern was incorporated into a three-dimensional (3D) gradient-echo sequence; aliasing then has an incoherent noiselike pattern rather than the usual coherent fold-over wrapping pattern. This k-space-sampling pattern was combined with a compressed sensing nonlinear reconstruction method that exploits the assumption of sparsity of medical images to permit reconstruction from undersampled k-space data and remove the noiselike aliasing. Thirty-four patients (15 female and 19 male patients; mean age, 8.1 years; range, 0-17 years) referred for cardiovascular, abdominal, and knee MR imaging were scanned with this 3D gradient-echo sequence at high acceleration factors. Obtained k-space data were reconstructed with both a traditional parallel imaging algorithm and the nonlinear method. Both sets of images were rated for image quality, radiologist preference, and delineation of specific structures by two radiologists. Wilcoxon and symmetry tests were performed to test the hypothesis that there was no significant difference in ratings for image quality, preference, and delineation of specific structures.ResultsCompressed sensing images were preferred more often, had significantly higher image quality ratings, and greater delineation of anatomic structures (P < .001) than did images obtained with the traditional parallel reconstruction method.ConclusionA combination of parallel imaging and compressed sensing is feasible in a clinical setting and may provide higher resolution and/or faster imaging, addressing the challenge of delineating anatomic structures in pediatric MR imaging.

Project description:PurposeTo develop a highly accelerated phase-contrast cardiac-gated volume flow measurement (four-dimensional [4D] flow) magnetic resonance (MR) imaging technique based on spiral sampling and dynamic compressed sensing and to compare this technique with established phase-contrast imaging techniques for the quantification of blood flow in abdominal vessels.Materials and methodsThis single-center prospective study was compliant with HIPAA and approved by the institutional review board. Ten subjects (nine men, one woman; mean age, 51 years; age range, 30-70 years) were enrolled. Seven patients had liver disease. Written informed consent was obtained from all participants. Two 4D flow acquisitions were performed in each subject, one with use of Cartesian sampling with respiratory tracking and the other with use of spiral sampling and a breath hold. Cartesian two-dimensional (2D) cine phase-contrast images were also acquired in the portal vein. Two observers independently assessed vessel conspicuity on phase-contrast three-dimensional angiograms. Quantitative flow parameters were measured by two independent observers in major abdominal vessels. Intertechnique concordance was quantified by using Bland-Altman and logistic regression analyses.ResultsThere was moderate to substantial agreement in vessel conspicuity between 4D flow acquisitions in arteries and veins (κ = 0.71 and 0.61, respectively, for observer 1; κ = 0.71 and 0.44 for observer 2), whereas more artifacts were observed with spiral 4D flow (κ = 0.30 and 0.20). Quantitative measurements in abdominal vessels showed good equivalence between spiral and Cartesian 4D flow techniques (lower bound of the 95% confidence interval: 63%, 77%, 60%, and 64% for flow, area, average velocity, and peak velocity, respectively). For portal venous flow, spiral 4D flow was in better agreement with 2D cine phase-contrast flow (95% limits of agreement: -8.8 and 9.3 mL/sec, respectively) than was Cartesian 4D flow (95% limits of agreement: -10.6 and 14.6 mL/sec).ConclusionThe combination of highly efficient spiral sampling with dynamic compressed sensing results in major acceleration for 4D flow MR imaging, which allows comprehensive assessment of abdominal vessel hemodynamics in a single breath hold.

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Compressed sensing for highly efficient imaging transcriptomics.

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Compressed sensing for highly efficient imaging transcriptomics.

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