Export parameters

Here are the available parameters for the export step:

Required

• -i <path to the 1st channel config> -i <path to the 2nd channel config> ...

Optional

• -f <output cube size>: sets the size of the output N5 cell (default is 128). The z-size is adjusted automatically with respect to the pixel resolution
• --min <xMin,yMin,zMin>: min coordinate of the export
• --max <xMax,yMax,zMax>: max coordinate of the export
• --blending: smoothes transitions between the tiles instead of making a hard cut between them
• --fill: fills the extra space with the background intensity value instead of 0
  • For raw data, the background value is retrieved from the flatfield attributes (which could be either estimated or user-specified value)
  • For deconvolved data, the background intensity is estimated automatically in each channel (similar to how it's estimated for raw data in the flatfield step)