Required Fields

There are no required fields.

Default Fields

Field Type Allowed Values Default Value
targetDirectory string any string './'
prefix string any string 'demo'
numberOfSynthesizedImages int any int >= 1 1
compression string ('none','lzw','packbits') 'none'
protein.cytonuclearflag string ('cyto','nuc','all') 'cyto'
verbose boolean (True,False) True
debug boolean (True,False) False
microscope string ('none','lzw') 'none'
synthesis string ('nuclear','framework','all') 'all'
protein.cytonuclearflag string ('cyto','nucleus','all') 'all'
sampling.method string ('disc','sampled') 'disc'
savePDF boolean (True,False) False
spherical_cell boolean (True,False) False
synthesis.diffeomorhic.maximum_iterations int any int 100
randomwalk boolean (True,False) False
framefolder string any string []
walksteps int any int 1
overlapsubsize double any non-neg double 0.3
overlapthresh double any non-neg double 2
rendAtStd double any non-neg double 2

Optional Fields

Field Type Allowed Values Default Value
sampling.method.density int any int []
resolution.cell 1x3 double array any 1x3 double array []
resolution.objects 1x3 double array any 1x3 double array []
instance.cell 2D/3D binary image binary valued image []
instance.nucleus 2D/3D binary image binary valued image []
tempdir string any string './temp'
walk_type string (‘willmore’,’brownian’,’density’) True
output.tifimages boolean (True,False) []
output.indexedimage boolean (True,False) []
output.SBML boolean (True,False) []
output.blenderfile boolean (True,False) []
output.blender.downsample double any non-negative double []