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https://github.com/ferreols/tipi4icy
tipi4icy is a collection of Icy plugins based on TiPi
https://github.com/ferreols/tipi4icy
blind-deconvolution deconvolution deconvolution-microscopy icy-plugins microscopy
Last synced: 23 days ago
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tipi4icy is a collection of Icy plugins based on TiPi
- Host: GitHub
- URL: https://github.com/ferreols/tipi4icy
- Owner: FerreolS
- License: gpl-2.0
- Created: 2014-10-21T15:17:40.000Z (about 10 years ago)
- Default Branch: master
- Last Pushed: 2023-10-17T15:10:57.000Z (about 1 year ago)
- Last Synced: 2024-03-19T11:20:31.845Z (9 months ago)
- Topics: blind-deconvolution, deconvolution, deconvolution-microscopy, icy-plugins, microscopy
- Language: Java
- Homepage:
- Size: 2.2 MB
- Stars: 11
- Watchers: 7
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
tipi4icy
========
Master:  [](https://zenodo.org/badge/latestdoi/25529468)
tipi4icy is a collection of classes to link [Icy](http://icy.bioimageanalysis.org/) and [TiPi](https://github.com/emmt/TiPi), a Java *Toolkit for Inverse Problems and Imaging*. Along with [microTiPi](https://github.com/FerreolS/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](https://www.docker.com/). The docker images of [SimpleDEMIC](https://hub.docker.com/r/ferreol/simpledemic/) and [EpiDEMIC](https://hub.docker.com/r/ferreol/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](http://icy.bioimageanalysis.org/index.php?display=startDevWithIcy).
## Javadoc
The javadoc is auto generated at each push and is [HERE](http://ferreols.github.io/tipi4icy)