Flatfield parameters

Here are the available parameters for the flatfield step:

Required

• -i <path to tile configuration file>

Optional

• --2d to generate 2D flatfields instead of 3D by default. 2D is recommended for acquisitions with a small number of tiles (less than 100)
• -b <number of histogram bins> (default is 256)
• -v <background intensity value>
• --min <min histogram value>
• --max <max histogram value>
• --crop <xMin,yMin,zMin,xMax,yMax,zMax> (default is null so the entire volume is used)

If -v / --min / --max are omitted, they will be estimated automatically from the image data.