2015-01-04: STSE is switching to Github.

After long time of hesitation (?!) we decided to switch to Github. Our SVN repository will be then frozen. The new git repository can be found here:

$ git clone

2014-01-01: STSE is supported by Scientific Center of Optical and Electron Microscopy at ETH Zurich.

STSE finally found its home! Now it will be developed and supported by Image & Data Analysis unit of Scientific Center of Optical and Electron Microscopy at ETH Zurich. We hope to be closer to data and community of biologists - two crucial in our eyes aspects - necessary to develop usable software.

2012-08-12: STSE is getting some new features for Yeast image processing.

These features will be committed to the official repository after publishing ;/ however one can see some excepts here. Also please contact us if you are interested in physical-based, growth models of yeast cells (imaging protocols, simulation protocols, modeling tools). Agent-based, physical simulation of Yeast colony growth. Simulation in the context of Game of Life Synthetic Biology project realized together with MIT Ron Weiss lab and INRIA Bang Team. People: Francois Bertaux, Gregory Batt, Dirk Drasdo, Allen Lin, Jingjing Sun, Ron Weiss, Szymon Stoma. Organizations: INRIA Contraintes/Bang (Paris, France), Weiss Lab@MIT (MA, USA). Status: Unpublished. Please click image to animate!

2011-12-02: Work for students!

Check here if you find anything interesting for you (partly PL for the moment...)!

2011-11-06: STSE presentation at CellProfiler home (Anne Carpenter group, Broad Institute, Boston, USA)

STSE initiative was presented to Anne Carpenter and her colleagues. For us it is an important place, since this is where MIT and Harvard images are mostly processed ;) We got some interesting feedback and perspectives. More news to come, so stay tuned! An example illustrating the spatial diffusion in the projection of the cell. A real cell geometry is used to calculate the evolution of the gradient through the time and space. Please click image to animate!

2011-06-24: New tutorials prepared for Virtualplants days on phyllotaxis.

New tutorials were prepared and presented during the days of Virtualplants (INRIA team) close to Montpellier. The tutorials can be found in SVN and they cover modeling meristems on various scales.

2011-04-04: STSE presented during the Unicellsys meeting in Mallorca (Spain).

STSE was presented in the slot dedicated to tools and methods. The title of the talk was: Spatio-Temporal Simulation Environment (STSE): a tool for microscopy image-based modeling. We met a bunch of nice people interested mainly in Systems Biology of the Yeasts and we hope to set up some successful collaborations.

2011-03-29: STSE use case paper finally accepted!

Finally we managed to have a formal reference for the tool. After more then 6 months waiting (sic!), a peer reviewed journal BMC Bioinformatics accepted our publication. Here is a reference (and proof read file linked):

"STSE: Spatio-Temporal Simulation Environment Dedicated to Biology", Stoma S, Froehlich M, Gerber S, Klipp E, BMC Bioinformatics, BMC Bioinformatics, 2011, 12(1):126.

2011-03-23: STSE will profit from Google Summer School of Code 2011

This summer we managed to succeed with the Google Summer School of Code 2011 application (please check our application here). Some functionality developed during this project will be integrated into STSE! Hurray, another hands to work!

2011-03-22: STSE presented during SystemTB conference in Prague.

The STSE software was introduced and presented to the community modeling Tuberculosis. The title was "Systematic model building: modeling in space and time" and the meeting took place in Prague (Czech Republic).

2011-02-07: Team programming@WPUT course finished!

We finished the course "Team programming" which was supposed to teach students how to work together on bigger projects. During this time we developed a few interesting extensions to STSE - the individual contributions might be found here.

2010-12-03: STSE presented at University of Wroclaw, Departament of Computer Science

Original note can be found here [PL]. After the lecture there was some time to discuss various aspects of bioinformatics. The slides from the presentation can be found here.

2010-11-27: Windows version of STSE!

Finally we checked all the dependencies and we are happy to announce that windows version is running (yes, the winter again...). Please remember that the instalation is still long and difficult, so the recommended way of testing the software is still via SBOS distribution ( Recommended ISO image ).

2010-11-25: Webpage refreshed...

Finally we found some time to refresh the webpage style (yes, the winter motivates us to have some colors, at least on the screen). Some content was also added (including credits).

2010-10-22: STSE is being developed by students as a part of the Team Programming subject @WPUT

We start to have a feedback from students at WPUT. Currently the projects are being defined and assigned to different groups. We hope to have some prototypes tested and implemented during this procedure. More to come soon! Subject page: Team Programming@WPUT

2010-08-15: STSE is going to be present in the 6th Workshop on Computation of Biochemical Pathways and Genetic Networks, Heidelberg (Germany), 2010

STSE is going to be presented in the session about new directions in Spatial Simulations. This will differ from all the previous STSE talks, since we plan to prepare a real "hands on" tutorial, and we will have plenty of time to discuss STSE workflow.

2010-08-08: STSE failed to receive the FNP grant

STSE did not receive the FNP grant despite the very good recommendations - we scored 5,4,4,3 which gives us the average of 4: "very good application - should receive funding". Please check our reviews here: 1 2 3 4. Despite this sad news, we are still willing to fight for this project and now we are considering new strategies learning from the previous experiences.. Stay tuned!

2010-08-05: STSE presented in Microscopy and Microanalysis, Portland (USA), 2010

STSE was presented in the session about Quantitative Microscopy, the feedbacks were positive. The main remarks suggested to consider using STSE not only for the Biology, but also for the material physics.. Yes, it was surprising.. ;]

2010-07-28: STSE presented in ERASysBio Data Management for Systems Biology, Adeje (Spain)

STSE was presented in a short session.

2010-06-02: STSE will be developed in WPUT

A various topics related to STSE development were accepted by WPUT didactic council. Starting from 10-2010 these topics will be developed by two groups of 12 students while the Team Programming course. We are happy to have more hands to work!

2010-05-18: STSE presented on Advanced Light Microscopy Techniques and Their Applications 10th International ELMI Meeting

STSE get some positive feedback from the community! We hope to get some interesting collaborations in the area of cell biology. Webpage of the conference leads to the proceedings.

2010-05-05: STSE project formally evaluated by FNP

We were informed that the STSE has passed the formal verification for Homing Plus grants. Now we are waiting for experts' reviews..

2010-04-20: STSE project submitted to FNP

STSE is trying to go its own way! ;] The project was submitted to Fundation for the Polish Science for the Homing Plus project, 2010. We know that there was about 60 submitted projects, the first ten will be funded. Project description can be found here.

2010-04-01: Video presentation availibed!

Videos demonstrating the image digitizations are online. Please check them out here.

2010-04-13: STSE accepted for Platform Presentation at Microscopy and Microanalysis, Portland (USA), 2010

We are happy to announce that you will able to hear us in August in USA this year. If you will be attending this conference, do not miss us!
Presenter: Stoma, Szymon
Platform Presentation Day: Thursday
Platform Presentation Date: 8/5/2010
Platform Presentation Time: 1:30:00 PM - 1:45:00 PM
Presentation Room (Oregon Convention Center): B117
Session ID: A14B
Symposium Title: Image Analysis & Quantitative Microscopy

2010-01-01: STSE moves to its new home!

STSE was moved from where it was started to its own domain

2009-04-08: Webpage started!

A wiki based resource is started for the STSE project. If you are here, you already know about it! ;]

2009-04-07: Initial code upload to SVN server

To get the newest code release issue:

svn co stse

2009-03-02: STSE project created!

So it begins! Please check