The repositories here include the codes used in publications from the lab of Prof. Kinneret Keren (Technion), primarily for image analysis in the context of Hydra regeneration.
The repositories include:
DisplayFunctions - Creating binary masks and image adjustment using CLAHE.
LayerSeparationFull - Separating signal from basal and apical surfaces in 3D stacks and creating 2D projection images from these signals.
EPySegAdapter - Our application of EPySeg, a package for segmenting cells in 2D epithelia: https://github.com/baigouy/EPySeg.
OrientationAnalysis - Extracting orientation field and further analysis of nematic fibre orientation.
PostSegmentationAnalysis - Quantification of cell-based measures from cell segmented images and tools for analysis in relation to fibre organisation.
MATLABUtilityFunctions - Supporting utility functions for all repositories.
References:
Maroudas-Sacks, Y., Garion, L., Shani-Zerbib, L., Livshits, A., Braun, E., Keren, K. Topological defects in the nematic order of actin fibres as organization centres of Hydra morphogenesis. Nat. Phys. 17, 251–259 (2021). https://doi.org/10.1038/s41567-020-01083-1
Livshits, A., Garion, L., Maroudas-Sacks, Y., Braun, E., Keren, K. Plasticity of body axis polarity in Hydra regeneration under constraints. Sci Rep 12, 13368 (2022). https://doi.org/10.1038/s41598-022-17411-9
Shani-Zerbib, L.; Garion, L.; Maroudas-Sacks, Y.; Braun, E.; Keren, K. Canalized Morphogenesis Driven by Inherited Tissue Asymmetries in Hydra Regeneration. Genes 2022, 13, 360. https://doi.org/10.3390/genes13020360
Maroudas-Sacks, Y., S Suganthan, Garion, L., Ascoli-Abbina, Y., Westfried, A., Dori, N., Pasvinter, P., Popović, M., Keren, K. Mechanical strain focusing at topological defect sites in regenerating Hydra. bioRxiv 2024.06.13.598802; doi: https://doi.org/10.1101/2024.06.13.598802
Maroudas-Sacks, Y., Garion, L., S Suganthan, Popović, M., Keren, K.. Confinement modulates axial patterning in regenerating Hydra. bioRxiv 2024.06.13.598813; doi: https://doi.org/10.1101/2024.06.13.598813
- The codes are provided here for reference and are annotated for accesibility, but have been developed primarily for internal use, so are not intended to be further supported beyond publication.