Step by step Guide for eC-CLEM AutoFinder Automatic registration 2D with spots. DatasetManon.

Open both light images: here nuclei at different magnifications Drag and drop

Find what can be common in both modalities In this example, nuclei appears mostly as spots in the bigger field of view, we will use spot detection 1.

1. If there were any ROI on your image, erase it.

1

Launch the spot detector On the Big image, select Channel 0 (DAPI) for the detection Spot detector Bright Spot over dark background, Sacel about 7 pixels

2

Select Output/Export to Roi

1

spot detector On the small image, select Channel 0 (DAPI) for the detection Spot detector Bright Spot over dark background, Add a Scale about 13 pixels : because of the difference of resolution: we do not want to separate too much the nuclei Select Output/Export to Roi

2

1

Autofinder Close spot detector, select Autofinder. Warning: here the pixel size is about 2 um for the target image, 1 micron will not be enough. Select 10 microns instead. Select find small Part in Bigger field of view ,

check Also show the transformed target on source. 2 good candidates wer found (orange circles) at the same position.

Check the results 1.

Source registered on Target show the position (with a small rotation here)

1

Check the results 1.

Target registered on Source.

2.

You can link both image to show exactly the same position in both image with your mouse by selecting lock 1 in both images.

1 1