Commit 2bc881d7 authored by Mark Winter's avatar Mark Winter
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Updated readme with new links

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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](LICENSE.md) 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.
Unless otherwise noted, the software and code in this repository is licensed under the GPL-v3 license. See [`LICENSE`](LICENSE.md) 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](https://git-bioimage.coe.drexel.edu/bioimage/leverjs) lineage editing and visualization tool, and [Hydra](https://git-bioimage.coe.drexel.edu/bioimage/hydra-image-processor) a CUDA-based image processing library.
The algorithms here are dependent on several related projects. The [`LEVER`](https://git-bioimage.coe.drexel.edu/bioimage/leverjs) lineage editing and visualization tool, and [`Hydra`](https://git-bioimage.coe.drexel.edu/bioimage/hydra-image-processor) a CUDA-based image processing library. Additionally, the MATLAB utilities library [`matlab-utilities`](https://git-bioimage.coe.drexel.edu/opensource/matlab-utilities) is required. All three libraries should be downloaded and placed on the local machine MATLAB path.
The main algorithms for identification of calcium vesicles are in the [+Segment](+Segment) folder. The segmentation algorithm [leverjs_seg_dataset](+Segment/leverjs_seg_dataset.m) runs on LEVER database structures.
The main algorithms for identification of calcium vesicles are in the [`+Segment`](+Segment) folder. The segmentation algorithm [`leverjs_seg_dataset`](+Segment/leverjs_seg_dataset.m) runs on LEVER database structures.
Tools for extracting size and motion statistics are in the [+Stats](+Stats) folder. All analysis code used the MATLAB 2019b programming language.
Tools for extracting size and motion statistics are in the [`+Stats`](+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.
### Sample Datasets
In addition to this source code repository, several example datasets from the paper have been made available through the Zenodo open science platform at: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4382712.svg)](https://doi.org/10.5281/zenodo.4382712).
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