iannellog
commented
4 years ago Try to read section 1.8 of the TeraTools Guide. In particular your case should be the one described in the second part of the section and in Appendix C. I understand the the procedure could be explained better, but at the moment I have not a better documentation. One important thing is that you cannot use a TIFF format as output with all 4 channels since we do support only TIFF RGB. However you can choose which channel must be excluded using the option --clist (this is also explained in section 1.8 of the Guide).
Hello. I want to replace the last step (merge) of Terastitcher with Teraconverter, but with different sets of images. I am trying to figure out how to use it.
I have 4 channel images, and I computed the displacements using 1st channel. Now I want to stitch remaining 3 channels using the displacements computed from Terastitcher on the 1st channel. From the first channel, I got 5 xml files (attached xmls.zip)
In the TeraTools documentation, Sec 2.4 mentions that an xml file can be given as an input to the Teraconverter. So if I understand correctly, for my scenario, I have to use these arguments,
--s : source file containing 3D tiff files of ch4 (e.g.), made in the two level hierarchy format --d : output directory (something new) --sfmt : xml file generated using Terastitcher --import step on the ch4 two level hierarchy format, i.e. --s option (import.pdf) --dfmt : "TIFF (series, 2D)" (a string) --resolutions=0 (I only want the full resolution) -f=graylevel (each channel is 16bit) --imin_plugin="tiff3D" (my input ch4 tiled images are 3D bigtiff images) --imout_plugin="tiff2D"
However, I don't know where to use the placetiles.xml (attached, generated from step 5 of Terastitcher on ch1), because placetiles.xml has the displacement information.
Could you please let me know what I am missing? Thank you.