Correlia: an ImageJ plug‐in to co‐register and visualise multimodal correlative micrographs

Summary The correlation of different microscopic imaging techniques alongside with microanalytical methods is crucial to better understand biological processes on a subcellular level. For that, micrographs and chemical maps exhibiting both, very different spatial resolution and field‐of‐view but also a highly multimodal content has to be co‐registered. We developed the ImageJ/Fiji plug‐in Correlia that provides an environment for handling multimodal correlative microscopy data. Several linear and nonlinear registration methods using either feature or area‐based similarity measures can flexibly be cascaded to align and warp 2D microscopy data sets. The registration of data sets containing light‐ and electron micrographs as well as chemical maps acquired by secondary‐ion mass spectroscopy and energy‐dispersive X‐ray spectroscopy is demonstrated. Correlia is an open‐source tool developed particularly for the registration and analysis of highly multimodal 2D correlative microscopy data. Lay Description If a microscopic object is imaged correlatively by two or more different microscopes the acquired micrographs will have to be overlaid accurately using an image‐registration software. In cases of relatively similar image content creating such an overlay is straight‐forward but what if the fields‐of‐view and resolutions of the micrographs differ significantly? What if there are distortions in a micrograph which have to be corrected before creating an overlay? What if furthermore a chemical map shall be overlaid that merely shows regions in which a certain chemical element is present? The rapidly increasing number of applications in correlative microscopy is calling for an easy‐to‐use and flexible image registration software that can deal with these challenges. Having that in mind, we developed Correlia, an ImageJ/Fiji plug‐in that provides an environment for handling multimodal 2D correlative microscopy data‐sets. It allows for creating overlays using different registration algorithms that can flexibly be cascaded. In this paper we describe what is happening ‘under the hood’ and give two example data‐sets from microbiology which were registered using Correlia. Correlia is open source software and available from www.ufz.de/correlia ‐ including introductory examples, as the authors would like to encourage other scientists to process their individual correlative microscopy data using Correlia.