[1] D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz, R. Guiet, C. Vonesch, M. Unser, "DeconvolutionLab2 : An OpenSource Software for Deconvolution Microscopy" Methods, in press, 2017. 
Download  Instruction to start  
Deconvolution  
Java Standalone 
DeconvolutionLab_2.jar 
Download DeconvolutionLab_2.jar, do not unzip it.

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


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 32bits and 64bits machines, and Linux 32bits and 64bits machines. 
Download the FFTW.zip folder, unzip it and put it in the same directory than DeconvolutionLab_2.jar 
Algorithms  Shortname  Iterative  Step Controllable  Regularization  Wavelets 
Deconvolution  
Regularized Inverse Filter Laplacian Regularized Inverse Filter 
RIF LRIF 
Direct  No  Yes  
Tikhonov Regularized Inverse Filter  TRIF  Direct  Yes  
Naive Inverse Filter Inverse Filter 
NIF IF 
Direct  No  Yes  
RichardsonLucy  RL  Iterative  No  No  
RichardsonLucy Total Variation  RLTV  Iterative  No  Yes  
Landweber Linear Least Squares 
LW LLS 
Iterative  Yes  No  
Nonnegative Least Squares Landweber+Positivity 
NNLS LW+ 
Iterative  Yes  No  
BoundedVariable Least Squares SparkParker 
BVLS SP 
Iterative  Yes  No  
Van Cittert  VC  Iterative  Yes  No  
TikhonovMiller  TM  Iterative  Yes  Yes  
Iterative Constraint TikhonovMiller  ICTM  Iterative  Yes  Yes  
FISTA  FISTA  Iterative  No  Yes  Haar, Spline 
ISTA  ISTA  Iterative  No  Yes  Haar, Spline 
Simulation  
Simulation  SIM  Direct  
Convolution  CONV  Direct  
Identity  I  Direct  
Nonstabilized Division  DIV  Direct 
The results of the deconvolution in terms of image reconstruction are the same than our previous version DeconvolutionLab. DeconvolutionLab2 improves the usability through friendly userinterface and it run on various imaging platform It offers a larger choice a FFT librairies and different ways to cancel the border artefacts. In addition, it allows a scripting for batch processing.
The command line of DeconvolutionLab2 consists of a series of arguments that allows a full control of the processing. The command line is written in a single line, space is mostly used as separator. The general format of the argument is:
keyword [option] parameters
The list of keywords and the options presenting in the following table. The sign  indicate a OR). The default value are written in bold
Keyword  Default  Options  Description  
Mandatory  
image  file  directory  synthetic  platform  Name of the input image  
psf  file  dir  directory  synthetic  platform  Name of the psf  
algorithm  I 
RIF  TRIF  NIF  LW  NNLS  BVLS  RL  RLTV  TM  ICTM  ISTA  FISTA  VC  I  CONV  SIM  DIV
Synonym of the acronym: RIF = LRIF, NIF = IF, LW = LLS, NNLS = LW+, BVLS = SP, I = ID 
Name and parameter of the algorithm  
Running  
path  current  current  path  Working directory  
stats  show  show  save  no  Statistics  
verbose  log  log  quiet  prolix  mute  Message monitoring  
monitor  console table  console  table Êno  Selection of the monitoring output  
display  yes  yes  no  The final results is displayed  
multithreading  yes  yes  no  
system  yes  yes  no  
Iterative Controller (every @n iteration, only at the end by default)  
time  no  no  value  Limitation of running time  
residu  no  no  value  Stops when the minimal residu is reached  
constraint  no  no  nonnegativity  clipped  Spatial constraint on the signal  
reference  no  no  filename  Assess the current deconvolved image with the reference image  
Output (several instances of out are possible)  
out stack  intact float 
Name of the output: Note that this name is used as title of the window image and as the filename for the storage Option for dynamic: intact  rescaled  normalized  clipped Option for type: byte  short  float Mode: By default the output is shown and saved. nosave  noshow 
Output as a stack of images (TIF)  
out series  intact float  Output as series of 2D images (slices, XY)  
out mip  intact float  Output as a maximumintensity projection  
out ortho  intact float  Output as a 3 orthogonal views centered around the keypoint  
out planar  intact float  Outputs as a 2D sidetoside image of all the zslices  
Border  
pad  NO NO 0 0  NO  X2  X23  X235  E2  Lateral and axial padding and extension scheme  
apo  NO NO  UNIFORM ÊNO ÊHAMMING  HANN  COSINE ÊTUKEY  WELCH  Lateral and axial apodization window function  
Computation  
norm  1  no  value  Normalization factor for the PSF  
fft  fastest  academic  jtransforms  fftw2  Indicates the FFT library  
epsilon  1E6  value  Machine Epsilon 
Material  Download  Size  Description  
Deconvolution  
Slide in PDF (without the animation/video)  3DDeconvolutionMicroscopy.pdf  4.6 Mb  Course given in Neubias 2020, February 2017  
Restoration  logo.zip  0.6 Mb  2D simulation, influence of the PSF shape to restore the original image  
Naive Inverse Filter  naivedeconvolution.zip  3.3 Mb  2D simulation of the inverse filter  
Simulation to check the resolution  testresolution.ijm  0 Mb  Macro to generate simulated data and simulated PSF  
Simulation to check the spectral effect  spectralanalysis.zip  0.7 Mb  2D simulation of fine structures  
Hollow bars  bars.zip  28 Mb  3D reference, 3D corruputed data and 3D PSF  
Celegans embryo  celegans.zip  183 Mb  3 fluoresence channels, 3D data and 3D theoretical PSF  
Synthetic microtubules  microtubuleschallenge.zip  63 Mb  3D data and 3D theoretical PSF of a realistic specimen  
Drosophila (crop)  drosophilacrop.zip  19 Mb  Small 3D data and 3D theoritical PSF  
Synthetic microtubules  realdonut.zip  463 Mb  3D data and 3D estimated PSF of real welldefined objects (donut) 
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© 2017 EPFL • webmaster.big@epfl.ch • 12.02.2017