eLife Paper on Refractive Index Matching in Live Imaging

Microscopes are optimized to give the clearest images, taking great care of all optical components along the light path. This has lead to a situation where the transition between a live sample and the surrounding liquid becomes the biggest imperfection in the optical path.

In this MPI-CBG/MPI-PKS/CSBD collaboration, lead by Tobias Boothe from the Rink lab, we show a simple but highly effective procedure to minimize the optical imperfection at the sample/medium interface. The technique is based on OptiPrep (chemical name: iodixanol), which can be ordered and used in any biological laboratory without any unusual equipment. Our technique worked with no toxicity or other problems in whole animals, primary cells, cell lines, as well as organoids.

Find our paper online with eLife.

Methods Article in ‘Development’

We are happy to post about our lab’s recent publication in Development. The article describes how to label and analyze single mRNA molecules, within single cells, at different stages of the zebrafish embryo’s development. With this technique, we hope to open new avenues into gene expression patterns and cellular differentiation programs.

The project was chiefly driven Carine Stapel, currently a PhD student in the Vastenhouw Lab. Carine developed the experimental protocol. The associated, freely available image analysis and quantification pipeline was developed in collaboration with Gene Myer’s research group as well as the Scientific Computing Facility. In fact, all work was done in-house at the MPI-CBG, demonstrating the institute’s wide array of qualifications as well as its collaborative spirit.

The article and protocol are available from Development, and the article also contains the analysis pipeline in its Supplementary Information. Article Page at Development

Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos

L. Carine StapelBenoit LombardotColeman BroaddusDagmar KainmuellerFlorian JugEugene W. MyersNadine L. Vastenhouw;