Reconstruction Parameters

API

ReconParams

type	object
properties
otf_file	Otf File
	OTF file
	default	None
	anyOf		type	string
			format	file-path
			type	null
usecorr	Usecorr
	use the flat-field correction file provided
	type	boolean
	default	False
ndirs	Ndirs
	number of directions
	type	integer
	default	3
nphases	Nphases
	number of phases per direction
	type	integer
	default	5
nordersout	Nordersout
	number of output orders; must be <= norders
	type	integer
	default	0
angle0	Angle0
	angle of the first direction in radians
	type	number
	default	1.648
ls	Ls
	line spacing of SIM pattern in microns
	type	number
	default	0.172
na	Na
	Detection numerical aperture
	type	number
	default	1.42
nimm	Nimm
	refractive index of immersion medium
	type	number
	default	1.515
zoomfact	Zoomfact
	lateral oversampling factor
	type	number
	default	2
explodefact	Explodefact
	artificially exploding the reciprocal-space distance between orders by this factor
	type	number
	default	1
zzoom	Zzoom
	axial zoom factor
	type	integer
	default	1
nofilteroverlaps	Nofilteroverlaps
	do not filter the overlaping region between bands usually used in trouble shooting
	type	boolean
	default	False
background	Background
	camera readout background
	type	number
	default	0
wiener	Wiener
	Wiener constant
	type	number
	default	0.01
forcemodamp	Forcemodamp
	modamps forced to these values
	default	None
	anyOf		type	array
			items
				type	number
			type	null
k0angles	K0Angles
	user given pattern vector k0 angles for all directions
	default	None
	anyOf		type	array
			items
				type	number
			type	null
otfRA	Otfra
	using rotationally averaged OTF
	type	boolean
	default	True
otfPerAngle	Otfperangle
	using one OTF per SIM angle
	type	boolean
	default	True
fastSI	Fastsi
	SIM data is organized in Z->Angle->Phase order; default being Angle->Z->Phase
	type	boolean
	default	True
k0searchAll	K0Searchall
	search for k0 at all time points
	type	boolean
	default	False
norescale	Norescale
	bleach correcting for z
	type	boolean
	default	False
equalizez	Equalizez
	bleach correcting for z
	type	boolean
	default	True
equalizet	Equalizet
	bleach correcting for time
	type	boolean
	default	True
dampenOrder0	Dampenorder0
	dampen order-0 in final assembly
	type	boolean
	default	True
nosuppress	Nosuppress
	do not suppress DC singularity in final assembly (good idea for 2D/TIRF data)
	type	boolean
	default	False
nokz0	Nokz0
	do not use kz=0 plane of the 0th order in the final assembly
	type	boolean
	default	True
gammaApo	Gammaapo
	output apodization gamma; 1.0 means triangular apo
	type	number
	default	1
bessel	Bessel
	bessel-SIM data
	type	boolean
	default	False
besselExWave	Besselexwave
	Bessel SIM excitation wavelength in microns
	type	number
	default	0.488
besselNA	Besselna
	Bessel SIM excitation NA)
	type	number
	default	0.144
deskew	Deskew
	Deskew angle; if not 0.0 then perform deskewing before processing
	type	number
	default	0
deskewshift	Deskewshift
	If deskewed, the output image’s extra shift in X (positive->left)
	type	integer
	default	0
noRecon	Norecon
	No reconstruction will be performed; useful when combined with –deskew
	type	boolean
	default	False
cropXY	Cropxy
	Crop the XY dimension to this number; 0 means no cropping
	type	integer
	default	0
xyres	Xyres
	XY pixel size
	type	number
	default	0.1
zres	Zres
	Z step size
	type	number
	default	0.2
zresPSF	Zrespsf
	Z step size of the PSF
	type	number
	default	0.15
wavelength	Wavelength
	emission wavelength in nanometers
	type	integer
	default	530
writeTitle	Writetitle
	Write command line to image header (may cause issues with bioformats)
	type	boolean
	default	False