Several software and tools have been developed (or co-developed) by the SRP and PhD students during the project:
- SPITFIRE (SParse fIT for Fluorescence Image Restoration): software designed to restore 2D-3D+Time fluorescent microscopy images and videos, and subtract undesirable out-of-focus background. Inter Deposit Digital Number: IDDN.FR.001.460029.000.S.P.2021.000.21000 – URL: https://github.com/sylvainprigent/spitfire – Publication: https://hal.inria.fr/hal-03518618
- DenseMapping (Dense mapping of diffusion and drift of moving particles): software designed to to estimate the diffusion and drift parameters attached to moving biomolecules within cells from 2D/3D individual trajectories. Inter Deposit Digital Number: IDDN.FR.001.290028.000.S.P.2021.000.21000 – URL: https://team.inria.fr/serpico/densemapping – Publications: https://hal.inria.fr/hal-03087048
- STracking: Open-source Python library for combining algorithms into standardized particles tracking pipelines for biological microscopy images. URL: https://github.com/sylvainprigent/napari-stracking – Publication: https://hal.inria.fr/hal-03688217
- LineageD: hybrid web-based system to predict, visualize, and interactively adjust plant embryo cell lineages. Users can build the hierarchy tree in two directions, bottom-up and top-down. Also, they can check and correct assignments based on Machine Learning predictions. URL: https://plantembryo.saclay.inria.fr/, https://plantembryoml.saclay.inria.fr/ – Publication: https://hal.inria.fr/hal-03699221
- ctrl (Cell Tracking and Robust Lineaging): Python package providing tracking methods to compute cell lineages in 3D+T images of growing plant tissues. URL: https://gitlab.inria.fr/mosaic/work-in-progress/ctrl/-/tree/develop – Publication: https://hal.inrae.fr/hal-03683119
GNOMON project – The MOSAIC, SERPICO/STED and HYBRID teams have collaborated in order to build a software (GNOMON, https://gnomon.gitlabpages.inria.fr/gnomon, ongoing since 2018, License LGPL3, 2021-2024), dedicated to the analysis, visualization, and simulation of morphogenesis of living organisms and intracellular dynamics. We made a special effort to make bridges with the technical solution developed in the BioImageIT project (https://bioimageit.github.io) focused on interoperability between software and data management in one hand, and on the other hand, with the web-based 3D+Time browser MorphoNet (https://morphonet.org/). The aim was to reach a software quality that will enable the diffusion of the platform, starting with the immediate collaborators of the partners. The software is currently entering a phase of beta-testing among close collaborators of the team, who will provide some key feedback on real use cases.
