[ITK] [ITK-dev] method of concatenating 2D images into a 5D image

[Tim Jackson]

Hi everyone,

I've recently started working with a very large .nd2 format time lapse
image, that was taken on a Nikon confocal microscope.  These image
sequences are 5D (x,y,z,time,channel).  Because these images are so large,
trying to work on the entire image at once will cause a memory allocation
error.  Therefore I set the reader up in ITK, use a series of
ExtractImageFilters to break down the giant file into 2D images (I iterate
over the time sequence in a for loop, obtaining a 2D x, y image for each
time frame for each channel).

This all works fine, and I'm able to complete the necessary image
filtering/corrections on these 2D images within the for loop.  My problem
arises when I'm trying to write the output file.  Ideally, I would like to
be able to compose all of these images back into one large 5D .nd2 file,
but if I do this outright, I'm guessing the writer will have a memory
allocation error.  Is there a way to write the file one frame at a time,
adding the next frame onto the file as the filtering occurs?  Or is there
some other way to handle the writing of very large image files to skirt
around memory allocation problems?  I know I could write each frame as an
individual file in an image sequence, but then I would have to use a
third-party program like ImageJ to make them into a stack, merge channels,
etc, which is not a simple task with the volume of image files I will be
analyzing.

Thanks for your help!
Tim
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