MRI's Redmine

The accounting system of mri. Users buy hours that are counted down when they use resources of the facility.

Problématique d'analyse d'images :
- Mesure d'intensité de spots dans le temps
- Tracking de cellules avec division / segmentation
- Lineage

The goal of this project is the migration of the FISH-quant software from MATLAB to python.
FISH-quant is a program written in Matlab for analyzing single molecule mRNA FISH data. It allows counting the number of mature and nascent transcripts in 3D images. ...

Matlab scripts for doing image analysis written at the MRI facility

MRI offers a workshop "Image analysis with ImageJ". This projects serves to develop the workshop and to make the different documents available.

ImageJ macros for biological image analysis

”Cell Image Analyzer” adds a visual scripting interface to ImageJ’s capabilities, which allows creating applications from
existing operations by drag and drop. It provides support to create batch applications as well as interactive
applications. ”Cell Image Analyzer” is used at the microscopy facility Montpellier RIO Imaging to create custom...

Libs for MRI projects

MRI currently uses a modified version of grr (http://grr.mutualibre.org/). This project aims at first updating the version of grr while keeping our modifications. Then at adding new features specific for MRI.

Development of the new website of the MRI facility, based on JOOMLA.

Application permettant de faire un logoff windows dans un temps défini par l'utilisateur

Portail d'inscription et gestion des utilisateurs

Different small projects that support the quality management at MRI.
- global login
- dysfunction warning
- autonomy system
- efficiency data in glpi
...

The project allows to communicate with a distant huscript. In order to do so a server that communicates via a socket is implemented in tcl. The server manages sessions. A user can start a session from the distance on the server, send a number of commands that are executed in huscript, get the results back and close the session. ...

Remote-ImageJ allows to run ImageJ macros on a remote machine. The communication between distant ImageJ-plugins is based on a custom messaging middleware called “Simple Java Message Exchange” (SIJAME). The SIJAME-server listens on a socket and handles each incoming connection in a separate thread. Based on the SIJAME-middleware a Remote-Macro-Runner has been written. The Remote-Macro-Runner-Server-Console allows to start and stop the server and to view log-messages. The Modal-Dialog-Killer avoids that modal dialogs, opened by a macro or by an error in a macro, block the macro execution on the server. A local macro is run on a distant machine, with the help of the remote-macro-runner-client-application. To set input files and folders, and output folders, using a JFileChooser-dialog and a list-editor, the IOSettings-plugin is used. These settings are accessible from within the macro. The RemoteFilesystemView implements a filesystem-view as a proxy that gets its information from a remote machine....

Central Image Database and Analysis tools.
WIDE is a software development project initiated and run by Montpellier Rio Imaging. It aims mainly at facilitating the management of the data produced by the resources of the facility, all driven by a computer (microscopes, flow cytometers and cell sorters, XR microtomograph). All acquired data can be uploaded into WIDE. They can then easily be managed on the WIDE website, using any computer that has an internet connection....