Visualizing and Comparing Machine Learning Predictions to Improve Human-AI Teaming on the Example of Cell Lineage

Hong, Jiayi; Maciejewski, Ross; Trubuil, Alain; Isenberg, Tobias

doi:10.1109/tvcg.2023.3302308

IEEE Trans. Visual. Comput. Graphics

2024

DOI: 10.1109/tvcg.2023.3302308

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Visualizing and Comparing Machine Learning Predictions to Improve Human-AI Teaming on the Example of Cell Lineage

Jiayi Hong,

Ross Maciejewski,

Alain Trubuil

et al.

Abstract: HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des labor… Show more

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TreeJ: an ImageJ plugin for interactive cell lineage reconstruction from static images

Laruelle,

Palauqui,

Andrey

et al. 2023

Plant Methods

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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.

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TreeJ: an ImageJ plugin for interactive cell lineage reconstruction from static images

Laruelle,

Palauqui,

Andrey

et al. 2023

Plant Methods

View full text Add to dashboard Cite

show abstract

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Visualizing and Comparing Machine Learning Predictions to Improve Human-AI Teaming on the Example of Cell Lineage

Cited by 1 publication

References 45 publications

TreeJ: an ImageJ plugin for interactive cell lineage reconstruction from static images

TreeJ: an ImageJ plugin for interactive cell lineage reconstruction from static images

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