Posted by
Kenneth Sloan-2 on
Dec 28, 2018; 11:28pm
URL: http://imagej.273.s1.nabble.com/registration-tools-tp5021591.html
I seem to have confused myself. I don't remember how I got into this confusion, so I'm asking
for guidance.
We do a lot of image registration. For stacks of images captured using the same methods, we generally
use SIFT. But, we also deal with multi-modal images, where gray-levels may be reversed, and "matching
features" don't obviously "match". In those cases, we rely on user input to select common landmarks.
Often, the images to be registered are different types (RGB, 8-bit, Float) and sizes.
Some time ago, I wrote a plugin that accepts 1, 2, or 3 landmarks in each image, and uses "barycentric" interpolation
to define a mapping from one image to the other. When 1 common landmark exists, only Translation is used; when 2, I use Translation, Rotation, and Scale; when 3 are supplied, I do a more general transformation which maps the two triangles
onto each other exactly. (Actually, I always match two triangles, but when only 1 or 2 common landmarks are provided I construct artificial landmarks to create a complete triangle in each image).
Virtually always, it turned out that 2 landmarks (giving a TRS transformation) was what we needed. I then "discovered"
the "align with Line Roi" plugin. This has worked just fine.
Now, however, I can't tell WHERE I found it - and I'm having trouble giving instructions to users who want to install
everything we need on their many machines.
So...is this plugin included in the standard FIJI distribution? Or, must it be manually added?
Second - when I search for it, I find it, with documentation that says it only handles gray images. The one I have
installed handles RGB images (and seems to change the source image to match the target). Hence, my confusion...
While I have you - I would appreciate expert guidance as to the "best" tool for this job. Again, the requirements are:
a) handles all image types (preferably by NOT requiring or enforcing all images to be the same type)
b) uses user input to provide 1,2,3, (or more?) matching landmarks
And, of course, where to find your preferred plugin.
Note: for image STACKS, I suppose all images will already be the same size and type. For multi-modal images, my
preference is to register the images one-at-a-time against a single master image. Changing the SIZE of the
source image to match the target is OK, but I would prefer to NOT be forced to match image TYPE. But...the images
will probably eventually end up in a Stack, so it's not too onerous to use a common type (as long as RGB is supported).
In general, I prefer RGB for all color images, and tend to prefer Float for grayscale images.
My fallback will be to revive and harden my BarycentricRegistration plugin - but I'm trying to use "standard" tools where available.
--
Kenneth Sloan
[hidden email]
Vision is the art of seeing what is invisible to others.
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