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Bigwarp

Basics

  • Working with landmarks
  • Saving transformation
    • Saving landmarks
    • Exporting the transform as a deformation field
  • Exporting warped images
    • detailed options
  • General tips

Transforming points and ROIs

Fine-tuning an automatic transformation

  • Running Bigwarp starting from an automatic result

"Homework"

  • Confirm that the exported deformation field works properly.

A challenging task that brings it all together (cos7_clemSamples)

The goal is to apply a chain of transformations to high-resolution raw data to avoid interpolating multiple times. Two things

(A) Figure out how to apply the automatic transformation correctly

  1. Use transformix to convert BSplineParameters.txt to a deforamation field, ("dfield.tif")
  2. Apply the inverse of reorientation.mat to emZoomRaw.tif
  3. Apply dfield.tif to the result of (2).
  4. Make sure the result matches em.tif
  5. Concatenate dfield.tif and the inverse of reorientation.mat (make sure you get the order right).

(B) Use bigwarp to fine-tune the automatic result

Use bigwarp to improve the registration around the mito in emZoomRaw.tif

  1. Run bigwarp with em.tif as the moving image and PALM_532nm_lo.tif as the fixed image.
  2. Set landmarks to improve the registration around the mito of interest in emZoomRaw.tif.
  3. Save the landmarks.

(C) Concatenate and apply all the transformations

  1. Concatenate dfield.tif and the inverse of reorientation.mat