fix broken link to coloc course slides.
**The Zeiss 510 has a different pinhole per channel... and depending on their positions and correct setup, the images of the bead in different channels is also affected by pinhole position settings.
*Nowadays with the Zeiss 7xx series and on the Olympus FV1000 and other modern point scanners there is only 1 pinhole for the emission light, so that problem is suppressed.
**BUT, the 405 lasers come in through a different fibre than the Vis lasers.. and so there is a collimation adjustment to make
**Same for 2photon lasers.... getting the near UV and IR laser spots to coincide exactly with the
vis lines is hard...
*So its best to get is as close as is reasonably possible to do in hardware adjustments, then measure the residual error then correct for it.
**BUT, they will never be whole xy pixels or z slice shifts... forget that idea its too crude.
**see the 2 slides titled
"Check with multi-colour beads" at [
http:// ifn. mpi-cbg.de/ wiki/ifn/images/ 0/ 0d/QuantitativeColocAnalysis- 12- 2010.pdf Colocalization analysis course notes]
*Now we can use Erik M's TransformJ Translate plugin in Fiji/ImageJ to do a sub pixel resolution shift for for each channel, as we have measured those shifts [http://www.imagescience.org/meijering/software/transformj/translate.html TransformJ Translate]