Correlative Light and Electron Microscopy


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.

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This plugin allows to compute a similarity (translation/rotation/scaling and flipping) transform from pair of points. It is updating the transformed image interactively such that the user get immediate feedback. The transformation is saved and can be applied to any other stack/image. Non rigid deformation can also be applied in 2D or 3D.

3D/3D,2D/3D or 3D /2D can be handled .

3D ROI are enabled, and can be checked with the 3D vtk view (size of ROI can be changed using the ROI stroke width).

Some prealignment by rotating in 3D the volume is possible.

Transformations can be applied directly or combined through Block Protocols (search for apply transformation).

It's also provide information about the predicted Error (based on statistical prediction), either as a full color mapping, either on each points used as landmarks, and error on the discrepancy in position between points.

There are video tutorials available in the web.


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