Software

  • Atols (Adaptative Threshold Operator based on Level Sets): Download Atols.
  • Obj.MPP (Object detection using a Marked Point Process (in Python 3)): See dedicated page.
  • SMLM-CEL0 (Single Molecule Localization in Microscopy – Continuous Exact L0): Single molecule localization in microscopy based on a deconvolution algorithm with a L0-regularization term to promote sparsity. The continuous exact L0 (CEL0) functional is minimized using an iteratively reweighted L1 method (IRL1). This software has been tested within the SMLMS 2016 software benchmarking.
    Available at: http://github.com/esoubies/SMLM-CEL0
  • SPADE (Small Particle Detector): Python software for detecting a collection of small particles in an image. It is based on a marked point process modeling where the objects belong to a predefined dictionary of shapes. Originally, it has been developed within the ANR project RNAGRIMP for detecting granules in cell cytoplasms.
    Available at: http://pypi.python.org/pypi/small-particle-detection and http://gitlab.inria.fr/ncedilni/spade.
  • timagetk (Tissue Image Toolkit): Python package dedicated to image processing of multicellular architectures such as plants or animals, and intended for biologists, modelers and computer scientists. Morpheme has contributed to its development by providing a number of image processing tools.
    Available at: http://timagetk.readthedocs.io

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