TreeJ: an ImageJ plugin for interactive cell lineage reconstruction from static images
Abstract Background 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 o...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2023-11-01
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| Series: | Plant Methods |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13007-023-01106-x |
| _version_ | 1797559453853155328 |
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| author | Elise Laruelle Jean-Christophe Palauqui Philippe Andrey Alain Trubuil |
| author_facet | Elise Laruelle Jean-Christophe Palauqui Philippe Andrey Alain Trubuil |
| author_sort | Elise Laruelle |
| collection | DOAJ |
| description | Abstract Background 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. Results 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. Conclusions 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 . |
| first_indexed | 2024-03-10T17:45:40Z |
| format | Article |
| id | doaj.art-237b834a261d49ce967ea8a736820805 |
| institution | Directory Open Access Journal |
| issn | 1746-4811 |
| language | English |
| last_indexed | 2024-03-10T17:45:40Z |
| publishDate | 2023-11-01 |
| publisher | BMC |
| record_format | Article |
| series | Plant Methods |
| spelling | doaj.art-237b834a261d49ce967ea8a7368208052023-11-20T09:32:40ZengBMCPlant Methods1746-48112023-11-0119111010.1186/s13007-023-01106-xTreeJ: an ImageJ plugin for interactive cell lineage reconstruction from static imagesElise Laruelle0Jean-Christophe Palauqui1Philippe Andrey2Alain Trubuil3Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB)Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB)Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB)MaIAGE, INRAE, Université Paris-SaclayAbstract Background 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. Results 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. Conclusions 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 .https://doi.org/10.1186/s13007-023-01106-xCell lineageImage annotationImageJ software |
| spellingShingle | Elise Laruelle Jean-Christophe Palauqui Philippe Andrey Alain Trubuil TreeJ: an ImageJ plugin for interactive cell lineage reconstruction from static images Plant Methods Cell lineage Image annotation ImageJ software |
| title | TreeJ: an ImageJ plugin for interactive cell lineage reconstruction from static images |
| title_full | TreeJ: an ImageJ plugin for interactive cell lineage reconstruction from static images |
| title_fullStr | TreeJ: an ImageJ plugin for interactive cell lineage reconstruction from static images |
| title_full_unstemmed | TreeJ: an ImageJ plugin for interactive cell lineage reconstruction from static images |
| title_short | TreeJ: an ImageJ plugin for interactive cell lineage reconstruction from static images |
| title_sort | treej an imagej plugin for interactive cell lineage reconstruction from static images |
| topic | Cell lineage Image annotation ImageJ software |
| url | https://doi.org/10.1186/s13007-023-01106-x |
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