From 2bc881d7f8ba6e1dc28f4225a6522210daa53523 Mon Sep 17 00:00:00 2001 From: Mark Winter <mwinter@drexel.edu> Date: Wed, 20 Jan 2021 15:44:24 +0100 Subject: [PATCH] Updated readme with new links --- readme.md | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/readme.md b/readme.md index 6cc57b7..d97932f 100644 --- a/readme.md +++ b/readme.md @@ -4,13 +4,16 @@ 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: [](https://doi.org/10.5281/zenodo.4382712). -- GitLab