Différences
Ci-dessous, les différences entre deux révisions de la page.
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developpement:productions:logiciels:levelsetmethod [2014/12/05 10:42] sbarends |
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 | ||
| - | From left to right : original image, contour detect by LSM, watershed segmentation, cells detect by LSM | ||
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| - | {{ :developpement:productions:logiciels:levelsetmethod.png?nolink&650 |}} | ||
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| - | {{ :developpement:productions:logiciels:lsm.png?nolink&650 |}} | ||
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| - | {{ :developpement:productions:logiciels: |}} | ||