Short Description

Epifluorescence DEconvolution MICroscopy is a blind deconvolution tool for widefield fluorescence microscopy

Documentation

This plugin contains a blind (i.e. without PSF knowledge) deconvolution method for widefield fluorescence microscopy (a.k.a. epifluorescence) 3D data only. It implements the method described in:

Blind deconvolution of 3D data in wide field fluorescence microscopy, Ferréol Soulez, Loïc Denis, Yves Tourneur, Éric Thiébaut in Proc of International Symposium on Biomedical Imaging, May 2012, Barcelona, Spain.

The code is available here https://github.com/FerreolS/tipi4icy

The plugin is composed of three steps

Step 1:

Step 2:

Step 3:

 

 

 

DEMICS on server

Deconvolution is a memory and computation intensive task and it may not fit in end-users laptop. To process batches of large datasets, both plugins can be used without the Icy GUI on any server with Docker. The docker images of EpiDEMIC can be pulled from docker hub and executed using (for epidemic):

docker run --rm -v FOLDER:/data -e NAME='DATAFILE'   -e XMS=MEMORY ferreol/epidemic'

where:

  • FOLDER is the folder were the dataset is,
  • DATAFILE is the name of the file and
  • MEMORY is the memory size of the JVM (default: 10G).

All the parameters should be stored in an XML file datafile-param.xml in the same folder. This parameter file can be generated easily using the plugin in the Icy GUI. The result will be stored in the file datafile-dec.tif.

Resources needing this

One review on “EpiDEMIC

  1. Imperial College
    Evolution from the MitivBlindDeconvolution plugin. Easy to use and good results. Maybe lacking a step-by-step guide for optimisation and when to use Steps 1-3 or simple Step 1 then 3.

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Changelog

  • Version 1.1.0.4 • Released on: 2019-03-08 12:29:12
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    Description:

    Fix a bug in the parameter update made after computation

  • Version 1.1.0.3 • Released on: 2019-03-05 11:35:49
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    Description:

    Fix starting point initialization issue in protocol (thanks to Jurgen Kriel)

  • Version 1.1.0.2 • Released on: 2019-03-04 15:42:51
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    Description:

    - Fix size initialization in protocol mode (thanks to Jurgen Kriel)
    - Fix initialization bug when the number of phase/modulus coefs is 0

  • Version 1.1.0.1 • Released on: 2018-10-04 15:45:32
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  • Version 1.1.0.0 • Released on: 2018-03-07 11:33:30
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    Description:

    bump version to correspond to the github release

  • Version 0.0.1.13 • Released on: 2017-10-11 07:28:48
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    Description:

    Really fix reset PSF bug

  • Version 0.0.1.12 • Released on: 2017-09-20 10:12:06
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    Description:

    Fix reset PSF bug

  • Version 0.0.1.11 • Released on: 2017-09-19 14:11:22
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    Description:

    fix debug symbol

  • Version 0.0.1.10 • Released on: 2017-08-30 20:19:44
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    Description:

    Fix positivity flag bug in protocol. Thanks to A. Dufour

  • Version 0.0.1.9 • Released on: 2017-05-22 11:22:11
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    Description:

    Change Emergency stop
    Fix visualization during computation

  • Version 0.0.1.8 • Released on: 2017-05-16 12:04:11
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  • Version 0.0.1.7 • Released on: 2017-05-16 11:36:25
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  • Version 0.0.1.6 • Released on: 2017-05-10 13:54:08
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  • Version 0.0.1.5 • Released on: 2017-03-29 21:39:17
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  • Version 0.0.1.4 • Released on: 2017-03-22 14:28:45
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  • Version 0.0.1.3 • Released on: 2017-03-15 21:07:16
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  • Version 0.0.1.2 • Released on: 2017-03-15 08:47:44
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  • Version 0.0.1.1b • Released on: 2017-03-03 16:21:14
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  • Version 0.0.1.0b • Released on: 2017-03-03 15:42:39
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