Three-dimensional single-cell transcriptome imaging of thick tissues
Multiplexed error-robust fluorescence in situ hybridization (MERFISH) allows genome-scale imaging of RNAs in individual cells in intact tissues. To date, MERFISH has been applied to image thin-tissue samples of ~10 µm thickness. Here, we present a thick-tissue three-dimensional (3D) MERFISH imaging...
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| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2024-12-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/90029 |
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| author | Rongxin Fang Aaron Halpern Mohammed Mostafizur Rahman Zhengkai Huang Zhiyun Lei Sebastian J Hell Catherine Dulac Xiaowei Zhuang |
| author_facet | Rongxin Fang Aaron Halpern Mohammed Mostafizur Rahman Zhengkai Huang Zhiyun Lei Sebastian J Hell Catherine Dulac Xiaowei Zhuang |
| author_sort | Rongxin Fang |
| collection | DOAJ |
| description | Multiplexed error-robust fluorescence in situ hybridization (MERFISH) allows genome-scale imaging of RNAs in individual cells in intact tissues. To date, MERFISH has been applied to image thin-tissue samples of ~10 µm thickness. Here, we present a thick-tissue three-dimensional (3D) MERFISH imaging method, which uses confocal microscopy for optical sectioning, deep learning for increasing imaging speed and quality, as well as sample preparation and imaging protocol optimized for thick samples. We demonstrated 3D MERFISH on mouse brain tissue sections of up to 200 µm thickness with high detection efficiency and accuracy. We anticipate that 3D thick-tissue MERFISH imaging will broaden the scope of questions that can be addressed by spatial genomics. |
| format | Article |
| id | doaj-art-ff4fc3e1dfbb4817851400bc2b11c40c |
| institution | DOAJ |
| issn | 2050-084X |
| language | English |
| publishDate | 2024-12-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj-art-ff4fc3e1dfbb4817851400bc2b11c40c2025-08-20T02:50:48ZengeLife Sciences Publications LtdeLife2050-084X2024-12-011210.7554/eLife.90029Three-dimensional single-cell transcriptome imaging of thick tissuesRongxin Fang0https://orcid.org/0000-0003-0107-7504Aaron Halpern1Mohammed Mostafizur Rahman2Zhengkai Huang3Zhiyun Lei4Sebastian J Hell5https://orcid.org/0009-0006-6291-9639Catherine Dulac6https://orcid.org/0000-0001-5024-5418Xiaowei Zhuang7https://orcid.org/0000-0002-6034-7853Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Center for Brain Science, Harvard University, Cambridge, United StatesHoward Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Center for Brain Science, Harvard University, Cambridge, United StatesHoward Hughes Medical Institute, Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, United StatesHoward Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Center for Brain Science, Harvard University, Cambridge, United StatesHoward Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Center for Brain Science, Harvard University, Cambridge, United StatesHoward Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Center for Brain Science, Harvard University, Cambridge, United StatesHoward Hughes Medical Institute, Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, United StatesHoward Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Center for Brain Science, Harvard University, Cambridge, United StatesMultiplexed error-robust fluorescence in situ hybridization (MERFISH) allows genome-scale imaging of RNAs in individual cells in intact tissues. To date, MERFISH has been applied to image thin-tissue samples of ~10 µm thickness. Here, we present a thick-tissue three-dimensional (3D) MERFISH imaging method, which uses confocal microscopy for optical sectioning, deep learning for increasing imaging speed and quality, as well as sample preparation and imaging protocol optimized for thick samples. We demonstrated 3D MERFISH on mouse brain tissue sections of up to 200 µm thickness with high detection efficiency and accuracy. We anticipate that 3D thick-tissue MERFISH imaging will broaden the scope of questions that can be addressed by spatial genomics.https://elifesciences.org/articles/90029spatial genomicsMERFISHbraingenome-scale imagingthick-tissue imagingspatial transcriptomics |
| spellingShingle | Rongxin Fang Aaron Halpern Mohammed Mostafizur Rahman Zhengkai Huang Zhiyun Lei Sebastian J Hell Catherine Dulac Xiaowei Zhuang Three-dimensional single-cell transcriptome imaging of thick tissues eLife spatial genomics MERFISH brain genome-scale imaging thick-tissue imaging spatial transcriptomics |
| title | Three-dimensional single-cell transcriptome imaging of thick tissues |
| title_full | Three-dimensional single-cell transcriptome imaging of thick tissues |
| title_fullStr | Three-dimensional single-cell transcriptome imaging of thick tissues |
| title_full_unstemmed | Three-dimensional single-cell transcriptome imaging of thick tissues |
| title_short | Three-dimensional single-cell transcriptome imaging of thick tissues |
| title_sort | three dimensional single cell transcriptome imaging of thick tissues |
| topic | spatial genomics MERFISH brain genome-scale imaging thick-tissue imaging spatial transcriptomics |
| url | https://elifesciences.org/articles/90029 |
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