RS-FISH: Precise, interactive, fast, and scalable FISH spot detection
| Item Type: | Preprint |
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| Title: | RS-FISH: Precise, interactive, fast, and scalable FISH spot detection |
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| Creators Name: | Bahry, E. and Breimann, L. and Zouinkhi, M. and Epstein, L. and Kolyvanov, K. and Long, X. and Harrington, K.I.S. and Lionnet, T. and Preibisch, S. |
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| Abstract: | Fluorescent in-situ hybridization (FISH)-based methods are powerful tools to study molecular processes with subcellular resolution, relying on accurate identification and localization of diffraction-limited spots in microscopy images. We developed the Radial Symmetry-FISH (RS-FISH) software that accurately, robustly, and quickly detects single-molecule spots in two and three dimensions, making it applicable to several key assays, including single-molecule FISH (smFISH), spatial transcriptomics, and spatial genomics. RS-FISH allows interactive parameter tuning and scales to large sets of images as well as tera-byte sized image volumes such as entire brain scans using straight-forward distributed processing on workstations, clusters, and in the cloud. |
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| Keywords: | smFISH, Image Analysis, Spatial Transcriptomics, Transcription, Spatial Genomics, Microscopy, Animals, Caenorhabditis elegans |
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| Source: | bioRxiv |
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| Publisher: | Cold Spring Harbor Laboratory Press |
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| Article Number: | 2021.03.09.434205v2 |
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| Date: | 18 October 2021 |
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| Official Publication: | https://doi.org/10.1101/2021.03.09.434205 |
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