Correlative Light and Electron Microscopy



Relate is a correlative software package optimised to work with EM, EDS, EBSD, & AFM data and images.  It provides the tools you need to correlate data from different microscopes, visualise multi-layered data in 2D and 3D, and conduct correlative analyses.

  • Combining data from different imaging modalities (e.g. AFM, EDS & EBSD)

  • Interactive display of multi-layer correlated data

  • Analytical tools for metadata interrogation

  • Documented workflows and processes


  • Import data from AZtec using the H5oina file format
  • Import AFM data
  • Correlate both sets of data using intuitive image overlays and image matching tools
  • Produce combined multimodal datasets


  • 2D display of multi-layered data
  • 3D visualisation of topography combined with AFM material properties, EM images, and EDS & EBSD map overlays
  • Customisation of colour palettes, data overlays, image rendering options, and document display
  • Export images and animations


  • Generate profile (cross section) views of multimodal data
  • Measure and quantify data across multiple layers
  • Analyse areas via data thresholding using amount of x-ray counts, phase maps, height, or other material properties.
  • Select an extensive range of measurement parameters
  • Export analytical data to text or CSV files
Relate analysis workflow example

Correlia is an open-source ImageJ/FIJI plug-in for the registration of 2D multi-modal microscopy data-sets. The software is developed at ProVIS - Centre for Correlative Microscopy and is specifically designed for the needs of chemical microscopy involving various micrographs as well as chemical maps at different resolutions and field-of-views.


This Fiji plugin is a python script for CLEM registration using deep learning, but it could be applied in principle to other modalities. The pretrained model was learned on chromatin SEM images and fluorescent staining, but a script is also provided to train an new model, based on CSBDeep. The registration is then performed as a feature based registration, using register virtual stack plugin (which extract features and then perform RANSAc. Editing the script in python gives access to more option (such as the transformation model to be used, similarity by default. Images need to be prepared such that they contain only one channel, but channel of ineterst (to be transformed with the same transformation) can be given as input, and Transform Virtual Stack plugin can be used as well.

F1000R Figure 1 DeepCLEM

MoBIE (Multimodal Big Image Data Exploration) is a framework for sharing and interactive browsing of multimodal big image data. The MoBIE Fiji viewer is based on BigDataViewer and enables browsing of MoBIE datasets. 

It is also called Platybrowser, and uses the n5 format.


Bigwarp is a tool for manual, interactive, landmark-based deformable image alignment. It uses the BigDataViewer for visualization and navigation, and uses a Thin Plate Spline implemented in Java to build a deformation from point correspondences.

Bigwarp screenshot