Classification of trajectoire: need tracking results as input and will then classify the trajectories asĀ  brownian motion, confined brownian or directed.

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intelligent Matrix Screener Remote Control


Integrates hardware control of Leica microscopes (via CAM), image analysis (e.g. via ImageJ, Matlab), and adaptive automatic screening of identified regions of interest.



Scipion is an image processing framework for obtaining 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents a unified interface for both biologists and developers. Scipion allows you to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on.



WormGUIDES Atlas is an interactive 4D portrayal of neural development in C. elegans. It will ultimately contain nuclear positions for every cell in the embryo, identified and tracked from the 2 cell stage until hatching. Single-cell and subcellular information, including neural outgrowth dynamics for each cell as well as cell function, gene expression, the adult neural connectome and related literature will be collated for each cell from public sources and also integrated with the atlas model. WormGUIDES Atlas integrates tools for exploratory data analyses and insight sharing. Navigation is linked between 3D and lineage tree views. In both contexts, community single cell information can be accessed with a click, creating live web queries that summarize knowledge about a cell. In many cases this information can be used to control cell color, creating customized interactive visualizations. A user's insights can be annotated directly into the embryo model with a note-taking interface that attaches each annotation to a cell or other point in space and time. These multi-dimensionally located notes can then be ordered into a (chrono)logical story sequence that explains developmental events as they unfold in the embryo. Annotations can be saved and shared with collaborators or the community.

WormGuides screenshot

Focal Adhesion Analysis Server


The website implements a set of computer vision algorithms designed to automatically process time-lapse images of fluorescently labeled focal adhesion proteins in motile cells. The methods associated with the processing have been published in PLOS One and Cell.

The publication describes a quantitative analysis of focal adhesion dynamics that have been imaged using TIRF. All image processing steps are well explained or referenced.

To better understand the dynamic regulation of focal adhesions, we have developed an analysis system for the automated detection, tracking, and data extraction of these structures in living cells. This analysis system was used to quantify the dynamics of fluorescently tagged Paxillin and FAK in NIH 3T3 fibroblasts followed via Total Internal Reflection Fluorescence Microscopy (TIRF). High content time series included the size, shape, intensity, and position of every adhesion present in a living cell. These properties were followed over time, revealing adhesion lifetime and turnover rates, and segregation of properties into distinct zones.

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OMERO is a free, open source image management software. It is client-server based system which supports 5D images, including big images and high-content screening data. Data are stored on a server using relational database. They are accessed using 3 main clients, a desktop client, a web client and a command line tool. There are bindings from OMERO to other image analysis packages, like FLIMfit, OMERO.searcher. The data in OMERO are organized in groups. A user can be a member of one or more groups. This groups can be collaborative or private, there are 4 levels of permissions to access/edit/annotate/delete the data of other users.

The package is supported not only by community forums, but also by a dedicated team which helps users to solve their problems and deals with the bugs submitted via error submission system.


Open source, scalable software, Supports diverse sets of imaging applications and domains (EM,LM, HCS, DigPath) Cross-platform, Java-based application, API support for Java, Python, C++, Django, On-line Forums, Automatic QA and upload of software errors Multi-dimensional images, Web access, Free Demo-server accounts


Enterprise-scale software, so complex install, requires expertise, Actively developing API, Python scripts and functions still developing

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