Epifluorescence DEconvolution MICroscopy is a blind deconvolution tool for widefield fluorescence microscopy
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
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'
FOLDERis the folder were the dataset is,
DATAFILEis the name of the file and
MEMORYis 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