CLEM registration workflow

This page describes the CLEM registration workflow used for COSEM as of November 2021. The details are likely to change, as developments toward improving usability are ongoing.

Prerequisites

• Fiji
• elastix
• template-building
• transforms-fiji (Coming soon)
• TransformationBDV (Coming soon)

Preprocessing

• Decide whether to transform light or em image data
• Choose scale level from mito prediction pyramid.
• Perform rough alignment* (if needed)
  • Crop
  • Permute axes
• Draw mask (if needed)
• Blur mito predictions
  • this will be a script (TODO).
• Export moving and target images to nrrd

rough alignment details

If needed, the details / parameters of the transformations must be recorded. Using Marwan's tool, this is possible by simply exporting the transformation.

automatic registration

These steps run automatic registration with elastix and enable a user to select parameters that work best.

• Choose set of parameters
  • (probably use all available).
• Set up elastix script
• Run elastix script.
• Visualize all results, choose the best, note the transform.

fine-tuning

Determine if fine tuning is needed, if so:

• Run Bigwarp with the best result so far
• Place landmarks to desired registration accuracy
• Save landmarks

Export

• Decide the format / resolution / field of view of the export
  • probably N5, FOV corresponding to the target image, resolution corresponding to the original moving image resolution
• Edit the transformation script
  • Set resolution / fov parameters
  • Specify all transforms used (rough alignment, elastix, bigwarp)
  • Soon to be replaced by this fiji plugin ?
• Run the transformation script