Laruelle Elise, Palauqui Jean-Christophe, Andrey Philippe, Trubuil Alain
Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Route de Saint Cyr, 78000, Versailles, France.
MaIAGE, INRAE, Université Paris-Saclay, Domaine de Vilvert, 78350, Jouy-en-josas, France.
Plant Methods. 2023 Nov 16;19(1):128. doi: 10.1186/s13007-023-01106-x.
With the emergence of deep-learning methods, tools are needed to capture and standardize image annotations made by experimentalists. In developmental biology, cell lineages are generally reconstructed from time-lapse data. However, some tissues need to be fixed to be accessible or to improve the staining. In this case, classical software do not offer the possibility of generating any lineage. Because of their rigid cell walls, plants present the advantage of keeping traces of the cell division history over successive generations in the cell patterns. To record this information despite having only a static image, dedicated tools are required.
We developed an interface to assist users in the building and editing of a lineage tree from a 3D labeled image. Each cell within the tree can be tagged. From the created tree, cells of a sub-tree or cells sharing the same tag can be extracted. The tree can be exported in a format compatible with dedicated software for advanced graph visualization and manipulation.
The TreeJ plugin for ImageJ/Fiji allows the user to generate and manipulate a lineage tree structure. The tree is compatible with other software to analyze the tree organization at the graphical level and at the cell pattern level. The code source is available at https://github.com/L-EL/TreeJ .
随着深度学习方法的出现，需要一些工具来捕获和规范实验人员所做的图像注释。在发育生物学中，细胞谱系通常从延时数据中重建。然而，一些组织需要固定以便于观察或改善染色效果。在这种情况下，传统软件无法生成任何谱系。由于植物具有坚硬的细胞壁，其优势在于能在细胞模式中保留连续几代细胞分裂历史的痕迹。即便只有静态图像，也需要专用工具来记录这些信息。
我们开发了一个界面，以协助用户从三维标记图像构建和编辑谱系树。树中的每个细胞都可以被标记。从创建的树中，可以提取子树的细胞或具有相同标记的细胞。该树可以导出为与专用软件兼容的格式，用于高级图形可视化和操作。
用于ImageJ/Fiji的TreeJ插件允许用户生成和操作谱系树结构。该树与其他软件兼容，可在图形级别和细胞模式级别分析树的组织。代码源可在https://github.com/L-EL/TreeJ获取。
