Bundled Tubes Long Sequence

Updated 02 February 2013

Bundles of 8 tubes of 30 nm diameter
Sparse density, 81049 molecules on 12000 frames

Structure Sample

Snapshot

Tube description

Views of the sample

Fluorophores

View of fluorophores • 1

Z-Projection Count fluorophore at 16.0nm/pixel
Field of view	6400.0x6400.0	nm
Field of view	400x400	pixels
Thickness	100.00	nm

Z-Projection Count fluorophore at 2.541nm/pixel
Field of view	1016.28x1016.28	nm
Field of view	400.00x400.00	pixels
Thickness	100.00	nm

View of fluorophores • 2

Z-Projection Count fluorophore at 16.0nm/pixel
Field of view	6400.0x6400.0	nm
Field of view	400x400	pixels
Thickness	100.00	nm

Z-Projection Count fluorophore at 1.18nm/pixel
Field of view	472.07x472.07	nm
Field of view	401.00x401.00	pixels
Thickness	100.00	nm

Point-Spread Function

Parameters

Physical Model
Wavelength	723.00	nm
Numerical aperture (NA)	1.40
Diffraction limit	258.21	nm
Offset focal plane	0	nm
XY function	Gaussian
FWHM	258.21	nm
Z function	Exponential
Focal plane	1 x FWHM at 0.0 nm
Defocus plane	2 x FWHM at 300.0 nm
Computational Parameters
Pixelsize to PSF convolution	5.0	nm
Depth of the PSF	500.0	nm

Resolution: 5.0 nm per voxel

XY orthogonal section at focal plane z:0.0 nm

XZ orthogonal section at y:1030.0 nm

XY dimension: 2070.00x2070.00 nm

XZ dimension: 2070.00x500.00 nm

[2] PSF Generator An ImageJ plugin to generate 3D microscope Point-Spread Function (PSF).

Sequence

Parameters

Camera
Photon converter factor or Quantum efficiency (QE)	1.00	e^-/Ph.
QE = QE-Gain x QE-interacting [Ref. 1]
Resolution	64	pixels
Pixelsize	100.00	nm
Field of view	6400.00	nm
Optics
Wavelength	723.00	nm
Numerical aperture (NA)	1.40
Diffraction limit	258.21	nm
Drift
Derive	Disable
Shaking	Disable
Autofluorescence
Constant backround level (Mean)	0.00
Constant background level (Standard Deviation)	0.00
Location of the sources	Structure
Number of sources	2000
Gain of sources	30
Size of sources	200	nm
Diffusion of sources	1000	nm
Displacement of sources	500	nm
Defocus (max) of sources	1500	nm
Number of scales	5
Evolution in the sequence	Dynamic
Percentage of change	20	%
Noise
Read-out noise	Enable
‐ Distribution: Gaussian (stdev)	5.0
Dark noise	Enable
‐ Distribution: Poisson	1.0
Shot noise	Enable
‐ Distribution: Poisson	1.0
EM Gain	Enable
‐ Distribution: Multiplicative	1.41
Hot pixel	Disable
Dead pixel	Disable
Analog Digital Conversion
Electron conversion - Gain	1.00	DN/e^-
Electron conversion - Offset	0.00	DN
Baseline	100.00	DN
Saturation	16383.00	DN
Quantization	14-bit
Computational Parameters
Number of activated fluorophores	81049
Thickness	500.00	nm
Frames (interval:1)	From 1 to 12000
Multithreading	Off-1 Thread
Verbose mode	Talk
Pixelsize to PSF convolution	5.0	nm
Pixelsize for adding autofluorescence	100.0	nm
Pixelsize of the camera	100.0	nm
File format	TIFF 16-bits
Fluorophores SNR
	Min ..Max	Mean
Peak signal s	160.00..1076.00	361.09
Background sdev σ_b	8.77..140.11	22.22
SNR (s-b)/σ_b	0.09..77.35	13.05
PSNR s/σ_b	2.20..87.99	21.03
SNR_sb (s-b)/sqrt(σ_b²+σ_s²)	0.09..5.19	3.42