[Insight-users] Constructing 3D stack from 2D image series (with registration)

[Darren Weber]

We have a series of several thousand 2D microscope images:

img0001 ... imgN

A simple ITK program uses itkImageSeriesReader to stack the sequential
images into a 3D volume for output to a .vtk file.  Without any
coregistration of the image series, the result is a mess (as expected).

Another ITK program runs registration algorithm(s) on consecutive pairs of
images in the 2D image series (each pair of images is registered
independently of any other images in the series).  It outputs a transform
file for each image registration, using file names something like:

img0002to0001.xfm
img0003to0002.xfm
etc.

What is an efficient way to combine and apply these transforms using an ITK
pipeline to 'concatenate' the image series into a 3D stack?

My conception of how this might work, in outline, is:

a)  begin with img0001
apply transform: none

b) add img0002 to the stack
apply transform: img0002to0001.xfm

c) add img0003 to the stack
apply transform: img0002to0001.xfm
apply transform: img0003to0002.xfm
(How to concatenate transforms without resampling image data?)

d) add img0004 to the stack
apply transform: img0002to0001.xfm
apply transform: img0003to0002.xfm
apply transform: img0004to0003.xfm
(How to concatenate transforms without resampling image data?)

etc.


In this conception of the problem, the pair-wise registration transforms are
'concatenated' to propagate the registration through the entire series.
What is the most efficient way to do that in ITK?

Is it possible (or reasonable) to associate a transform object (or file)
with each 'element' of an itkImageSeriesReader?  If not, is there another
convention for creating an ITK filter pipeline or registration pipeline?

TIA and take care,
Darren
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