Correlative Light and Electron Microscopy


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

This is an example workflow of how to perform automatic registration by

- first detecting spots in both images using wavelet segmentation (with different scale according to the image scale)

- second using Ec-Clem autofinder to register both images

Click on a block to know more about a tool. Non referenced tools are non clickable.

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Workflow results

Automatic registration in 2D or 3D based on detection or binary mask. Takes images with detections already done on it.

logo autofinder