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Deconstructing Gastrulation at Single-Cell Resolution
Version 3 2022-02-14, 14:24
Version 2 2022-01-17, 19:38
Version 1 2022-01-17, 19:38
dataset
posted on 2022-02-14, 14:24 authored by Tomer SternTomer SternThis repository contains two main packages that were developed as a part of:
"Deconstructing Gastrulation at Single-Cell Resolution" by Tomer Stern, Stanislav Y. Shvartsman, and Eric F. Wieschaus, Princeton University, 2021.
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Package #1: Segmentation and tracking code and demo data.
To use it - download the file, unzip it, and follow the instructions on the "Instructions.docx" file.
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Package #2: Data analysis (includes code and data for plotting the analyses presented in the manuscript).
It contains whole embryo cell segmentation and tracking of the two embryos used in the referenced publications, as well as several extracted features, such as cell areas and intercalation events.
It also contains code assisting in loading the data, visualizing it, and calculating a variety of additional morphological attributes.
To use it, download the file, unzip all into a single directory, open the "DG_main_script" script in matlab, and follow the instructions at the top comment.
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For any questions / comments / assistance in setting the code up or using it, please feel free to contact me at:
tstern@princeton.edu
or:
stern.tomer@gmail.com
Happy gastrulation!