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Step 3 - Producing a 3D mnc file 

  1. Step 1-9 of the reconstruction process will output a pixel size in microns  to be used in the below script
  2. In a terminal, in the directory with the reconstructed tif files, run 
for i in filename__rec*.tif; do convert $i GRAY:-; done | rawtominc -transverse -short -unsigned -xstep pixel_size/1000 -ystep pixel_size/1000 -zstep pixel_size/1000 -xstart 0 -ystart 0 -zstart 0 -2 -clobber /path/to/output/dir/filename.mnc 1023 1024 1024

Note: Step 1 of the reconstruction process will output a pixel size in microns (see above) to be used in the above script       3. Open the reconstructed mnc file in OCCIViewer  to view your 3D image