RNA Detection pp 143-162 | Cite as

Detection and Automated Analysis of Single Transcripts at Subcellular Resolution in Zebrafish Embryos

Part of the Methods in Molecular Biology book series (MIMB, volume 1649)


Single molecule fluorescence in situ hybridization (smFISH) is a method to visualize single mRNA molecules. When combined with cellular and nuclear segmentation, transcripts can be assigned to different cellular compartments resulting in quantitative information on transcript levels at subcellular resolution. The use of smFISH in zebrafish has been limited by the lack of protocols and an automated image analysis pipeline for samples of multicellular organisms. Here we present a protocol for smFISH on zebrafish cryosections. The protocol includes a method to obtain high-quality sections of zebrafish embryos, an smFISH protocol optimized for zebrafish cryosections, and a user-friendly, automated analysis pipeline for cell segmentation and transcript detection. The software is freely available and can be used to analyze sections of any multicellular organism.

Key words

smFISH Zebrafish Cryosections Automated cell segmentation Transcript detection 



This work was supported by MPI-CBG core funding, a Human Frontier Science Program Career Development Award [CDA-00060/2012-C] to NLV; and a Boehringer Ingelheim Fonds PhD fellowship to LCS. We thank Pavel Vopalensky for critically reading the manuscript, Julia Eichhorn for taking photos of the sectioning procedure, and Jan Philipp Junker and Alexander van Oudenaarden for initial advice on smFISH.


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Copyright information

© Springer Science+Business Media LLC 2018

Authors and Affiliations

  1. 1.Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
  2. 2.Center for Systems Biology DresdenMax Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany

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