Dynamics and molecular control of calcium-vesicle motion during sea urchin skeletogenesis revealed by 4D lattice-light-sheet-microscopy
Source Code Repository
This is the open-source code repository submitted for review along with the paper "Dynamics and molecular control of calcium-vesicle motion during sea urchin skeletogenesis revealed by 4D lattice-light-sheet-microscopy."
License and Use
Unless otherwise noted, the software and code in this repository is licensed under the GPL-v3 license. See LICENSE for details. The repository is being released for read-only review along with the associated article and may be modified based on feedback from reviewers before final release.
Structure of the Repository
The algorithms here are built on several related projects. The LEVER lineage editing and visualization tool, and Hydra a CUDA-based image processing library.
The main algorithms for identification of calcium vesicles are in the +Segment folder. The segmentation algorithm leverjs_seg_dataset runs on LEVER database structures.
Tools for extracting size and motion statistics are in the +Stats folder. All analysis code used the MATLAB 2019b programming language.
Additional utilities for movie creation and file-import/export can be found in the other subfolders.