Workflow

Standalone (v. 1.10)

The BioEmergences automated image processing workflow is delivered as a standalone code that can be executed from the command line and, in part, from a graphical user interface. It starts by filtering the images and detecting the cell centers from local maxima, continues with an optional segmentation of the shapes of nuclei and membranes, and ends with a tracking of the cells' trajectories, producing a digital specimen in output.

Download Installation package for OS X (requires XCode installed)

Download Source files and installation scripts for Linux and OS X

The Java software is required to run the applications provided by BioEmergences. Please visit the Java website to download and install the latest version of Java. OS X users are invited to install Java for OS X 10.7 and above as well (Java for OS X 10.6 or Java for OS X 10.5).

Web Service

While the standalone version was crafted for convenient processing of small datasets on a laptop computer, there is no size limit on the data that can be uploaded to the BioEmergences web service, available at http://bioemergences.iscpif.fr/workflow/, which offers users customized assistance in addition to fast processing. The online workflow architecture relies on iRODS, an open-source data management software, and the OpenMOLE engine, a middleware platform facilitating the experimental exploration of complex systems models on a computing cluster, which leverages the power of the European Grid Infrastructure (EGI). Interested users are invited to request an account to obtain access to these facilities by sending an email to nadine.peyrieras@inaf.cnrs-gif.fr.