November 2021, LCB released MiSiC software, the first tool capable of automatically analyzing images of bacterial biofilms that can be found in our mouths, in hospitals or in the soil.
MiSiC is a tool that allows generating a segmentation mask from microscopic images of bacterial cells. MiSiC has the capacity to detect and segment bacterial cells in microcolonies and/or dense images, which is not achievable using intensity thresholds. MiSiC can handle a wide range of bacterial morphologies and microscope modalities such as phase contrast, brightfield and fluorescence. MiSiC functions upstream of specialised tools for bacterial cell biology dedicated to measuring cellular features like area, length, position, etc (some convenient tools for this are MicrobeJ and Oufti). A graphical user interface named ‘MiSiCgui”is available (see GitHub). The main advantages of MiSiC are :
● Provide a pre-trained model with general detection capacities under various imaging modalities
● Provide an easy parameter handling with a graphical user interface
More informations about MiSic : https://github.com/leec13/MiSiCgui