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3D Deconvolution Microscopy
BIG >  3D Deconvolution Microscopy
DECONVOLUTION

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» DeconvolutionLab

» DeconvolutionLab2

» PSF Generator

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DeconvolutionLab2

The remasterized Java deconvolution tool

DeconvolutionLab2 is freely accessible and open-source for 3D deconvolution microscopy; it can be linked to well-known imaging software platforms, ImageJ, Fiji, ICY (not yet implemented), Matlab (not yet implemented) and it runs as a stand-alone application. The backbone of our software architecture is a library that contains the number-crunching elements of the deconvolution task. It includes the tool for a complete validation pipeline. Inquisitive minds inclined to peruse the code will find it fosters the understanding of deconvolution.

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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.

Installation of DeconvolutionLab2

 

Download Instruction to start
Deconvolution

Java Stand-alone
DeconvolutionLab_2.jar Download DeconvolutionLab_2.jar, do not unzip it.

  1. Double-click on the DeconvolutionLab_2.jar file
  2. To run Deconvolutionlab2, enter the following command line in the terminal:
    java jar DeconvolutionLab_2.jar help

ImageJ
Download DeconvolutionLab_2.jar, do not unzip it. Put DeconvolutionLab_2.jar in the plugins folder and restart ImageJ.

  1. Plugins > DeconvolutionLab2_Lab: Start the complete user interface of DeconvolutionLab2
  2. Plugins > DeconvolutionLab2_Run: Run headless a deconvolution command given as a macro, if no macro it is run the Lab
  3. Plugins > DeconvolutionLab2_Launch: launch the GUI for a deconvolution command given as a macro, if no macro it is run the Lab

ImageJ2

Fiji

Matlab

Add DeconvolutionLab_2 in the java path

javaaddpath([matlabroot filesep 'java' filesep 'DeconvolutionLab_2.jar'])

then run a specific algorithm

result = DL2.RIF(image, psf, 0.10000000149011612 , '');


Icy
Not yet implemented
Java Source Code
GIT Repository git clone https://c4science.ch/diffusion/2075/deconvolution.git
Status Status of the development
FFT Libraries
JTransforms Visit the page of JTransforms
JTransforms is already included in Fiji and Icy
Get a JTransforms.jar file and put it in the same directory than DeconvolutionLab_2.jar
FFTW FFTW.zip
It is include the FFTW2 dynamic libraries
for Mac OSX, and Windows 32-bits and 64-bits machines, and Linux 32-bits and 64-bits machines.
Download the FFTW.zip folder, unzip it and put it in the same directory than DeconvolutionLab_2.jar

How to use Deconvolution2

 

Image

© 2017 EPFL • webmaster.big@epfl.ch • 12.02.2017