used in:
https://www.biorxiv.org/content/10.1101/2020.04.29.068023v1
based on:
We pre-trained a StarDist 3D model using the annotation of a Arabidopsis thaliana lateral root nuclei dataset provided in (Wolny et al., 2020) and https://github.com/wolny/pytorch-3dunet.
Wolny, A., Cerrone, L., Vijayan, A., Tofanelli, R., Barro, A.V., Louveaux, M., et al. (2020). Accurate and versatile 3D segmentation of plant tissues at cellular resolution. eLife 9**,** e57613. doi: 10.7554/eLife.57613.
tested with:
Arabidopsis flowers
H2B:mRuby2 was used for the visualization of somatic nuclei of Arabidopsis thaliana flower. The flower was scanned from eight views differing by 45° increments in a Zeiss Z1 light-sheet microscope (Valuchova et al., 2020). We used a single view to mimic a challenging 3D segmentation problem. Image files are available in the Image Data Resource (Williams et al., 2017) under the accession code: idr0077.
Valuchova, S., Mikulkova, P., Pecinkova, J., Klimova, J., Krumnikl, M., Bainar, P., et al. (2020). Imaging plant germline differentiation within Arabidopsis flowers by light sheet microscopy. Elife 9. doi: 10.7554/eLife.52546.
and
Williams, E., Moore, J., Li, S.W., Rustici, G., Tarkowska, A., Chessel, A., et al. (2017). The Image Data Resource: A Bioimage Data Integration and Publication Platform. Nat Methods 14(8), 775-781. doi: 10.1038/nmeth.4326.
Sample results:
Volume segmentation. In all images, segmented nuclei are assigned a unique random color. Side-by-side comparison of segmented somatic nuclei of Arabidopsis thaliana flowers obtained with the 3D_Iso_Basic model that was trained on a similar dataset. The red box marks the area that is shown enlarged in the right panel. The green line indicates the location of the yz-plane shown in below.