Or any good plugins for image J? We image in whole mount and take large (around 100um total) stacks, so MIP images don't always do it justice. Any advice would be much appreciated!
Dear Olivia,
I found the 3d Viewer plugin for Image J quite useful.
Best,Thomas
Dear Olivia,
Image J or Fiji are ideal solution if you have time and some experience with image processing especially with large dataset it is not always fast or reliable - if you look for commercial solutions please look at the products Imaris from Bitplane now owned by Oxford instruments (works perfect with large dataset) and Arivis - ArivisVision (excellent for large datasets). There are also other commercial solutions but most of them are not optimised for large datasets as the two mentioned.
with best regards Roger
3D Viewer plug-in for ImageJ is a good tool. If you have a problem with large stacks, you can always try to process it virtually.
If you need more advanced visualization/processing/calculation options I highly recommend AvizoFire from FEI SAS. The disadvantage is the price. However, they offer at least 2 weeks trial version.
You might want to go to Fiji. Fiji Is Just ImageJ, but open and IMHO nicer. http://fiji.sc/Downloadshttp://fiji.sc/Downloads The folks at LOCI have a lot of nice tools for what it sounds like you are trying to do. http://loci.wisc.edu
If you're still looking for software options for these problems, please take a look at my company Simpleware's current solutions at http://www.simpleware.com/.
Can any one suggest me which software to used to get a confocal microscopy image of cells on polymer scaffold as a whole?
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