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. Includes code adapted from Vahid K. Alilou (2024). FingerPrint Matching: A simple approach (https://github.com/alilou63/fingerprint).
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. If you use any of these, please cite our relevant publications.
