bunwarpJ headless alignment coefficients

fiji

#1

Hi All. We are aligning large images using Fiji’s bunwarpJ algorithm, and we are performing these alignments on our server as we need 180+ GB memory heaps to process the images. In order to do so, we have to perform alignments in a --headless mode. The alignments work well, but no alignment coefficients are printed because these are typically represented in the Fiji GUI. We would like to use these coefficients as a metric to quantile alignments into overall categories of good, mediocre, bad, etc based upon coefficient thresholds.

I have not come across any straight-forward way to save or view these coefficients without the GUI and was wondering if anyone knows a way to obtain them without going through a desktop GUI, as we do not have any with enough memory to process the alignments that way? Thank you for your responses in advance!