tipi4icy

Master:

tipi4icy is a collection of classes to link Icy and TiPi, a Java Toolkit for Inverse Problems and Imaging. Along with microTiPi is mainly used to implements the DEconvolution MICroscopy Suite.

DEconvolution MICroscopy Suite (DEMICS)

DEMICS is a collection of Icy plugins for deconvolution microscopy. It provides user friendly and state of the art blind deconvolution methods for fluorescence microscopy.

SimpleDEMIC

SimpleDEMIC is a simple non blind deconvolution plugin that uses total variation regularization. As it is non blind, it requires the knowledge of the PSF.

EpiDEMIC

EpiDEMIC stands for Epifluorescence DEconvolution MICroscopy. It is a blind deconvolution plugin for Epifluorescence / Widefield fluorescence microscopy. It requires only basic knowledge about the data (numerical aperture, wavelength, pixel size,...)

Automated batch processing

Protocols

Both plugins are compatible with Icy's protocols and can be easily added to any processing workflow.

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 SimpleDEMIC and 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.

Developers corner

Eclipse

This project can be used in Eclipse, just copy/clone it into Eclipse workspace, then from Eclipse:

File -> import -> Existing project in workspace and choose TiPi folder.

Then Eclipse should automatically accept it as a known project.

To add the needed libraries to TiPi Eclipse project, move all the jars into a folder. Then in eclipse:

Right clic on TiPi project in package explorer -> Properties -> Java Build Path -> Libraries -> Add External jar and select all Library jar

Icy in Eclipse

There is a plugin to launch quickly and easily Icy from eclipse here.

Javadoc

The javadoc is auto generated at each push and is HERE