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. (2021) MorphoGraphX 2.0: Providing context for biological image analysis with positional information. bioRxiv preprint.

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