Aligning and focus stacking a bunch of confocal images

imagej
extended-focus

#1

I have a bunch of pictures obtained from a confocal microscope. They are slightly misaligned, so an alignment is mandatory before applying focus stacking.

You can download a folder with an example here.

I first aligned the pictures by using the plug-in Template Matching > Align slices in stack…

Later on, I applied the Z Project option (Image > Stacks > Z Project).

The problem is that the results are unexpectedly poor. I would like you to download the pictures and try to replicate or get new routines in order to get well-aligned and well-focus-stacked pictures.

Any other option? Can I see your results and know which are your routines to get to your final image?


#2

Dear @antecessor,

  1. https://imagej.net/Correct_3D_Drift
  2. http://bigwww.epfl.ch/thevenaz/stackreg/
  3. for even more options: https://imagej.net/Category:Registration

Best,
Stefan