Data Sets

2.5D data set – tomato meristem

Kierzkowski_2012Tomato meristem confocal data. This file contains raw confocal stacks from two time points of a growing tomato meristem, taken 11h apart. The meristem was stained with PI and a DR5 auxin reporter was collected in a separate channel. Corresponding MorphoGraphX files (surface meshes and parent labeling) are also included, as an example of growth and signal analysis.

Data published in: Kierzkowski, D., Nakayama, N., Routier-Kierzkowska, A. L., Weber, A., Bayer, E., Schorderet, M., Reinhardt, D., Kuhlemeier, C. & Smith, R. S. (2012). Elastic domains regulate growth and organogenesis in the plant shoot apical meristem. Science, 335(6072), 1096-1099.

3D data set – Arabidopsis seedling

Bassel_2014Arabidopsis embryo confocal data. This file contains a raw confocal stack of the radicle of a mature Arabidopsis embryo. The seedling was cleared and stained with propidium iodide, the clarity of signal makes it a good example of data for 3D segmentation.

Data published in: Bassel, G. W., Stamm, P., Mosca, G., Barbier de Reuille, P., Gibbs, D. J., Winter, R., Janka, Holdsworth, M. J. & Smith, R. S. (2014). Mechanical constraints imposed by 3D cellular geometry and arrangement modulate growth patterns in the Arabidopsis embryo. PNAS, 11(23), 8685-8690.

2.5D data set – Arabidopsis sepal

Hervieux2016Arabidopsis sepal confocal data. This file contains a raw confocal stack of an 8 time point series of a live imaged Arabidopsis sepal. Segmented meshes and lineage files are included.

Data published in: Hervieux N, Tsugawa S, Fruleux A, Dumond M, Routier-Kierzkowska A-L, Komatsuzaki T, Boudaoud A, Larkin JC, Smith RS, Li C-B, Hamant O (2017) Mechanical Shielding of Rapidly Growing Cells Buffers Growth Heterogeneity and Contributes to Organ Shape Reproducibility. Current Biology 27, 3468–3479.

Strauss et al. 2021 – data sets

These files contain a raw confocal data, meshes and additional files for the MorphoGraphX 2.0 paper:

Hervieux 2016 Arabidopsis Sepal Fig 2D-F 2S1 6DE 6S1B 8ADE.tar.gz
Kierzkowski 2012 Tomato Meristem Fig5F-I.tar.gz
Kierzkowski 2019 Arabidopsis Leaf Fig5A-E 6S1A 8JK.tar.gz
MontenegroJohnson 2019 Arabidopsis Meristem Fig 3AC 3S1D.tar.gz
Strauss 2021 Arabidopsis Root Fig 2AB 3BD 3S1 7 7S1 8E 8S1A.tar.gz
Strauss 2021 Arabidopsis Flower Fig 1.tar.gz
Strauss 2021 Arabidopsis Gynoecium Fig 3EFGH 3S1EFG.tar.gz
Strauss 2021 Arabidopsis Meristem Fig8LM 8S2EF.tar.gz
Strauss 2021 Arabidopsis Root Fig8N 8S2A-D.tar.gz
Strauss 2021 Arabidopsis Seedling Fig 2C.tar.gz
Vijayan 2021 Arabidopsis Ovule Fig 1S1 4.tar.gz
Yoshida 2014 Arabidopsis Embryo Fig 8FGHI 8S1BCDE.tar.gz

Data used/published in: Strauss S, Runions A, Lane B, Eschweiler D, Bajpai N, Trozzi N, Routier-Kierzkowska AL, Yoshida S, Rodrigues da Silveira S, Vijayan A, Tofanelli R, Majda M, Echevin E, Le Gloanec C, Bertrand-Rakusova H, Adibi M, Schneitz K, Bassel G, Kierzkowski D, Stegmaier J, Tsiantis M, Smith RS. (2022) Using positional information to provide context for biological image analysis with MorphoGraphX 2.0.

Majda et al. 2022 – data set

Majda et al. 2022 OnionStretching.tar.gz

This archive contains raw data from MorphoRobotX extensometer and MorphoDynamX finite elements models for the paper:

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