Ci-dessous, les différences entre deux révisions de la page.
developpement:productions:logiciels:levelsetmethod [2014/12/05 10:02] cicaluga |
developpement:productions:logiciels:levelsetmethod [2015/01/07 10:04] |
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- | ====== Image segmentation : Optimization of Level Set Methods for biological image segmentation (LSM) ====== | ||
- | An automatic way to segment grayscale 3D images of cells. | ||
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- | * **Why ?** | ||
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- | To study plant morphogenesis, one need to follow the evolution of a plant during time. We can use real-time live imaging and image segmentation to reconstruct the plant development at a cell level. | ||
- | A first pipeline, MARS-ALT, has been develop by the RDP laboratory in collaboration with the Virtual Plants team (INRIA, Montpellier), as a part of the OpenAlea platform for plant modelling. The 3D image are assembled from the fusion of three confocal stacks, and cells are segmented using a watershed algorithm. With 3D segmented images of the same plant at different steps of development, ALT can reconstruct the lineage between cells. | ||
- | To improve the segmentation part of the pipeline, a new method was implement in 3 steps : | ||
- | * * Detect exterior shape of the organ with LSM | ||
- | * * Perform a watershed algorithm to have a first segmentation, given the exterior shape | ||
- | * * Improve segmentation by re-detecting each cell shape with LSM |