Collection of reference datasets
The benchmarking of SMLM software package mainly relies on the usage of common reference datasets, in particular synthetic datasets with known ground-truth.
Conditions of use These reference datasets are designed to be largely used by the developpers to validate software and by the users to check a software. Reference: Sage et al. Quantitative evaluation of software packages for SMLM, Nature Methods 12, 2015.
The synthetic sample has been created artificially using a 3D artificial structure shape. This shape represents a seashell of six branches with various fluorophore densities. The position of the fluorophores of exactly known. Some image sequences have additional noise.
The sequences of images that we provide here simulates the PALM acquisition process: for a long sequence (2500 images, 50000 activated fluorophores) and for a short sequence (100 images, 2000 activated fluorophores).
Two version of this samples, large and flat, are articifically created. and they are available as a z-stack of images for the thick sample and as a 2D image for the flat sample. In the spatial (XY) orientation they have the shape of seashell with 6 branches of differents intensities.
3D structure sample
The structure consists in 6 tubes in seashell shape. The 6 tubes have 6 levels of intensity to simulates various density of the density of fluorophores.
Simulation of acquisition
The particles are randomly put into a frame at coordinate corresponding to the structure of the sample. More particles are put into the voxels which have higher intensities. The PSF is the Gibson & Lanni model PSF with the following features:
Large sample view as 3D z-stack.
Noiseless frame sequence.
Flat sample view as 2D image.
Biomedical Imaging Group, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
Last update: 31 Mar 2017