eC-CLEM: A multidimension, multimodel software to correlate intermodal images with a focus on light and electron...

Correlative light and electron microscopy (CLEM) is a scientific method covered by a broad range of techniques. The path taken to explore a scientific question is often driven both by the question and the technology available. Yet, one common step to all CLEM workflows is the registration of the multimodal images to assign a fluorescent signal to an ultrastructure. The manual relocation and registration of light microscopy and electron microscopy images can be challenging and time-consuming (Muller-Reichert & Verkade, 2014). eC-CLEM is a free open-source software to address this step. eC-CLEM has been designed with an intuitive procedure and the manual registration has been extensively described in step-by-step protocols on the eC-CLEM webpage as well as video tutorials. In this book chapter, we focus our description on the "automatic registration" procedure, which requires some fine tuning. We recommend the user to first get familiar with eC-CLEM through the aforementioned tutorials. If large volume data sets or automatic tracking and controlling of microscopes are pursued by the user, going through the fine-tuning steps described in this chapter is worth the effort.