If you are finding the stitching portion of your workflow taking too long I have a shameless plug for our accelerated stitching plugin called MIST.
It accelerates image stitching (2D+t only) by optionally using FFTW and CUDA. The global image position optimization algorithm is different than Grid/Collection, but the pairwise translations are generated the same way (Phase-Correlation-Image-Alignment-Method). The MIST stitching results are generally comparable to the Grid/Collection plugin despite the difference in translation optimization algorithms.
Note: MIST can only handle image grids which have roughly constant overlaps between images, within a few percent. Also, I do not know what you consider a ‘very large’ dataset, but MIST has been tested with image grids up to 220x220 (at 1040x1392 pixel images).
MIST can stitch with or without the acceleration libraries. The update site download comes bundled with FFTW libraries for Windows (Mac/Linux require the user to compile/install FFTW). To use CUDA you need to have a NVIDIA GPU and the CUDA 6.5 toolkit installed.
source code: https://github.com/usnistgov/MIST
availability: update site within Fiji
Send me a message if you have any questions about the tool.
To convert the image position list MIST generates into a form TrakEM2 can import (for viewing large stitched images) I have the following Python script which builds a text file matching this TrakEM2 documentation.
folder = 'C:/MIST_Convert_Test/'
input_filename = 'img-global-positions-1.txt' # needs to be a MIST *-global-positions* txt file
output_filename = 'trakem2_position_list.txt' # needs to be a *.txt file to import into TrakEM2
# open file handles
input_fh = open(folder + input_filename,'r')
output_fh = open(folder + output_filename,'w')
for line in input_fh:
# strip out the additional information MIST saves leaving only "<img_name>, <x>, <y>, 0"
toks = str.split(line, ';')
img_name = toks[str.find(toks,':')+2:]
img_pos = toks[str.find(toks, '(')+1:len(toks)-1]
output_fh.write(img_name + ', ' + img_pos + ', 0\n')
# close file handles