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Space-timE RePresentation, Imaging

and cellular dynamics of

molecular COmplexes




Softwares

  • ATLAS: Vesicle segmentation method (2012-2014) (C/C++)
  • Backwarping: Warp sequence with parametric motion model (1995-2013) (C/C++)
  • C-CRAFT: Vesicle segmentation and background estimation (2014) (C/C++, Java)
  • Cryo-Seg: Segmentation of tomograms in cryo-electron microscopy (2010)
  • Flux estimation: Particle and intensity flux estimation (2015) (C/C++)
  • GenLoc3D: 3D high-precision gene localization algorithm in cell nuclei (2014-2015) (Java (ImageJ))
  • GcoPS: Colocalization analysis (2017) (Java)
  • HotSpotDetection: Robust detection of fluorescence accumulation over time in video-microscopy (2007-2008) (C/C++)
  • HullkGround: Convex Hull for background subtraction (2008-2009) (C/C++, Java)
  • KLTracker: Track vesicle and POI in image sequences (C/C++)
  • Motion2D: Estimate 2D parametric motion model (C/C++)
  • MS-Detect: Detecting moving objects in image sequences by background subtraction (2008/2011) (C/C++)
  • ND-SAFIR: Image Denoising for ND Images (2004-2009) (C/C++, Java, matlab / Linux, Windows, Mac OSX)
  • OpticalFlow: Optical flow (2012) (C/C++)
  • OWF: Non-local means and optimal weights for noise removal (Matlab)
  • PBED: Patch-Based Event Detection (2009) (C/C++)
  • QuantEv: Spatio-temporal distribution analysis (2017) (C/C++, Java)
  • TubuleJ: Toolbox to process electron cryo-microscope images of vitrified microtubules (2009) (Java)

Software Demonstration

An on-line version of the image processing algorithms has been developped using the Mobyle framework (Institut Pasteur, see http://mobyle.pasteur.fr/).

Many of our softwares (C-CRAFT, ATLAS, HOTSPOTDETECTION, HULLKGROUND, KLTRACKER, MOTION2D, MS-DETECT, ND-SAFIR, OPTICALFLOW…) are available at Mobyle@SERPICO mobyle web portal.

The web interface makes our image processing methods available for biologist users without any installation or configuration on their own. The size of submitted images is limited to 200 MegaBytes per user and all the results are kept 15 days. The web portal and calculations run on a server with 2 CPU x 8 cores, 64 GigaBytes of RAM.