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Lu C, Chen G, Song W, Chen K, Hee C, Nikan M, Guagliardo P, Bennett CF, Seth P, Iyer KS, Young SG, Qi X, Jiang H. Tool to Resolve Distortions in Elemental and Isotopic Imaging. J Am Chem Soc 2024; 146:20221-20229. [PMID: 38985464 DOI: 10.1021/jacs.4c05384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Nanoscale secondary ion mass spectrometry (NanoSIMS) makes it possible to visualize elements and isotopes in a wide range of samples at a high resolution. However, the fidelity and quality of NanoSIMS images often suffer from distortions because of a requirement to acquire and integrate multiple image frames. We developed an optical flow-based algorithm tool, NanoSIMS Stabilizer, for all-channel postacquisition registration of images. The NanoSIMS Stabilizer effectively deals with the distortions and artifacts, resulting in a high-resolution visualization of isotope and element distribution. It is open source with an easy-to-use ImageJ plugin and is accompanied by a Python version with GPU acceleration.
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Affiliation(s)
- Chixiang Lu
- Department of Chemistry, The University of Hong Kong, Pok Fu Lam, Hong Kong 999077, P. R. China
| | - Gu Chen
- Department of Chemistry, The University of Hong Kong, Pok Fu Lam, Hong Kong 999077, P. R. China
| | - Wenxin Song
- Departments of Medicine, University of California, Los Angeles, California 90095, United States
| | - Kai Chen
- School of Molecular Sciences, University of Western Australia, Perth 6009, Australia
| | - Charmaine Hee
- School of Molecular Sciences, University of Western Australia, Perth 6009, Australia
| | - Mehran Nikan
- Ionis Pharmaceuticals, Inc., Carlsbad, California 92010, United States
| | - Paul Guagliardo
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Perth 6009, Australia
| | - C Frank Bennett
- Ionis Pharmaceuticals, Inc., Carlsbad, California 92010, United States
| | - Punit Seth
- Ionis Pharmaceuticals, Inc., Carlsbad, California 92010, United States
| | | | - Stephen G Young
- Departments of Medicine, University of California, Los Angeles, California 90095, United States
- Human Genetics, University of California, Los Angeles, California 90095, United States
| | - Xiaojuan Qi
- Electrical and Electronic Engineering, The University of Hong Kong, Pok Fu Lam, Hong Kong 999077, P. R. China
| | - Haibo Jiang
- Department of Chemistry, The University of Hong Kong, Pok Fu Lam, Hong Kong 999077, P. R. China
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Kraft ML, Brunet MA, Gorman BL. Depth Correction of 3D SIMS Images of Mammalian Cells with Secondary Ion Images Captures the Effects of Differential Sputtering. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1957-1958. [PMID: 37612937 DOI: 10.1093/micmic/ozad067.1014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Mary L Kraft
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Melanie A Brunet
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Brittney L Gorman
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WAUnited States
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Brunet MA, Kraft ML. Toward Understanding the Subcellular Distributions of Cholesterol and Sphingolipids Using High-Resolution NanoSIMS Imaging. Acc Chem Res 2023; 56:752-762. [PMID: 36913670 DOI: 10.1021/acs.accounts.2c00760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
ConspectusCharacterizing the subcellular distributions of biomolecules of interest is a basic inquiry that helps inform on the potential roles of these molecules in biological functions. Presently, the functions of specific lipid species and cholesterol are not well understood, partially because cholesterol and lipid species of interest are difficult to image with high spatial resolution but without perturbing them. Because cholesterol and lipids are relatively small and their distributions are influenced by noncovalent interactions with other biomolecules, functionalizing them with relatively large labels that permit their detection may alter their distributions in membranes and between organelles. This challenge has been surmounted by exploiting rare stable isotopes as labels that may be metabolically incorporated into cholesterol and lipids without altering their chemical compositions, and the Cameca NanoSIMS 50 instrument's ability to image rare stable isotope labels with high spatial resolution. This Account covers the use of secondary ion mass spectrometry (SIMS) performed with a Cameca NanoSIMS 50 instrument for imaging cholesterol and sphingolipids in the membranes of mammalian cells. The NanoSIMS 50 detects monatomic and diatomic secondary ions ejected from the sample to map the elemental and isotopic composition at the surface of the sample with better than 50 nm lateral resolution and 5 nm depth resolution. Much effort has focused on using NanoSIMS imaging of rare isotope-labeled cholesterol and sphingolipids for testing the long-standing hypothesis that cholesterol and sphingolipids colocalize within distinct domains in the plasma membrane. By using a NanoSIMS 50 to image rare isotope-labeled cholesterol and sphingolipids in parallel with affinity-labeled proteins of interest, a hypothesis regarding the colocalization of specific membrane proteins with cholesterol and sphingolipids in distinct plasma membrane domains has been tested. NanoSIMS performed in a depth profiling mode has enabled imaging the intracellular distributions of cholesterol and sphingolipids. Important progress has also been made in developing a computational depth correction strategy for constructing more accurate three-dimensional (3D) NanoSIMS depth profiling images of intracellular component distribution without requiring additional measurements with complementary techniques or signal collection. This Account provides an overview of this exciting progress, focusing on the studies from our laboratory that shifted understanding of plasma membrane organization, and the development of enabling tools for visualizing intracellular lipids.
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