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3D Deconvolution Microscopy
BIG >  3D Deconvolution Microscopy
DECONVOLUTION

Outline

Open Software

» DeconvolutionLab2

» DeconvolutionLab

» PSF Generator

3D Reference Datasets

Benchmarking

Advanced Methods

Conditions of Use

Acknowledgment

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Simulation of Microtubules

This datasets is a realistic-looking synthetic dataset representing a network of microtubules in a cell. It corresponds the GFP channel of the dataset used for the challenge on 3D deconvolution microscopy. The ground-truth, the PSF and some results are freely accessible upon a request by email.

Download

Object Maximum Intensity Projection File to download, Description, Size
Ground-truth

ground-truth.tif.zip

Reference dataset, simulation
256x128x128, 32 bits
2Mb

Simulation

input.tif.zip

Test volume, reference convolves with the PSF, plus noise
256x128x128, 32 bits
23Mb

PSF

psf.tif.zip

Theoretical Point-Spread Functio
256x128x128, 32 bits
45Mb

Result of Regularized Inverse Filter
DeconvolutionLab2

rif-0.0005.tif.zip

Regularized Inverse Filter, λ=0.0005

Result of Landweber
DeconvolutionLab2

LW-1000.tif.zip

Landweber, N=1000

Result of Richardson-Lucy
DeconvolutionLab2

RL-500.tif.zip

Richardson-Lucy, N=500

Result of Richardson-Lucy Total-Variation
DeconvolutionLab2

RLTV-500-0.001.tif.zip

Richardson-Lucy Total-Variation, N=500 λ=0.001

Result of FISTA
DeconvolutionLab2

FISTA-180-0.1.tif.zip

FISTA N=180 λ=0.1

Result of Soulez
Ferréol Soulez

soulez.tif.zip

Participant to the challenge of deconvolution 2013 and 2014

Result of Biggs
Biggs

biggs.tif.zip

Participant to the challenge of deconvolution 2013 and 2014

Result of Huygens
SVI Huygens

huygens.tif.zip

Participant to the challenge of deconvolution 2013 and 2014

Reference

[1] D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz, R. Guiet, C. Vonesch, M. Unser, "DeconvolutionLab2 : An Open-Source Software for Deconvolution Microscopy" Methods, in press, 2017.

Conditions of use

You'll be free to use this software for research purposes, but you must not transmit and distribute it without our consent. In addition, you undertake to include a citation whenever you present or publish results that are based on it. EPFL makes no warranties of any kind on this software and shall in no event be liable for damages of any kind in connection with the use and exploitation of this technology.

© 2018 EPFL • webmaster.big@epfl.ch • 26.10.2018