Hi,
Which software would you recommend to do 3-d bio and medical image analysis/processing. I heard some good library in ImageJ, MATLAB, CellProfiler and ICY. Which one should I start learning first? Which software would you recommend if the image is coming from computed tomography?
I would recommend Fiji (ImageJ) for a starting point (https://fiji.sc/). This is ImageJ with a number of pre-downloaded packages and plugins for scientific applications. You can often also find open-source plugins that others have written and make use of them as well. I think ImageJ is the most user-friendly image analysis software of the ones you listed above, though it is probably also the most limited. Depending on what you need to do in terms of post-processing, you may find yourself needing to use MATLAB. I would only use CellProfiler if you want to do detailed cell-tracking over time. Here's one example of a group that used ImageJ for computed tomography image analysis that came up with a quick Google search (see below), but I'm sure you could also find papers that make use of MATLAB.Article An application of image processing techniques in computed to...
I recommend to use MATLAB or Amira. Both are powerful for this purpose. If you are looking for a freeware try FIJI.
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