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3D Deconvolution in Microscopy
Test dataset for algorithm validation
Bioimaging and Optics Platform [BIOP]Biomedical Imaging Group [BIG]

C. elegans embryo

This real dataset is composed of three stacks of images of a C. Elegans embryo. The deconvolution effects can be evaluated on different kinds of structures: extended objects (the chromosomes in the nuclei), filaments (the microtubules), and point-wise spots (a protein stained with CY3).


Statistics Mininum Maximum Mean μ Std deviation
CY3 Channel 215 2842 992.34 595.23
FITC Channel 209 2929 657.66 327.59
DAPI Channel 205 2687 585.75 290.13


PSF Features
Refractive indexni: 1.518
Numerical apertureNA: 1.4
Spherical aberrationW040: 0
WavelengthDAPI:477nm; FITC:542nm; CY3:654nm
Spatial resolutiondeltar: 64.5 nm
Axial resolutiondeltaz: 160 nm

Image size: 672x712 pixels

Number of z slices: 104 slices

Number of channels: 3

Dynamic: 16 bits

Image format: TIFF

Microscope Acquisition: Olympus CellR

  • Objective: UPlanSApo 100X/1.4 oil(n.i. 1.518); image pixel size (binning 1X1): 64.5 nm
  • Laser intensity: 100% - Camera pixel size: 6450 nm - Gain: 0
  • z step: 200 nm (experiment 10, 1344x1024x111; crop 672x712x104)
  • Channel 1: DAPI, lamda excitation: 377/50 nm, lamda emission: 447/60 nm; Channel 2: FITC, lamda excitation: 485/20, lamda emission: 531/22; Channel 3: CY3,lamda excitation: 560/25,lamda emission: 634/40
Orthogonal previewMontage previewIndividual download

C-Elegans Embryo

Preview in RGB (Red:CY3, Green:FITC, Blue:DAPI)

XY section
ZY section
XZ section