Multi-scale imaging and analysis identify pan-embryo cell dynamics of germlayer formation in zebrafish
This repository contains the code to analyse and visualize cellular dynamics as presented in
- Shah,G. et al. (2017) Pan-embryo cell dynamics of germlayer formation in zebrafish. bioRxiv, 173583. preprint available at bioRxiv
Data can be found as a zip archive (678 MB) at https://imbcloud.medizin.tu-dresden.de/sharing/rN3K4YIub Unzipping the file from within the main folder creates the default test-data subfolder that is used in the notebook examples. If you choose another location for the data, the notebooks need to be adapted accordingly.
The link seems to be broken, we will provide a new link to the zip archive soon!
The image data (3D + time, 3 channels) for sample 1 is available for download at IDR. Processed cell tracks to reproduce the plots in the notebooks is available at (link coming soon)
As an alternative we have the parsed TGMM-based cell tracks. You can find the CSV files here: https://www.dropbox.com/scl/fo/ayg165lzgwe0jgsnll8gg/h?dl=0&rlkey=uj0xtr7w2w25oncoxrjon2w61
We have unfiltered cell tracks for the three samples. The cell data is exported as a data table with columns x, y, z, t, cell layer id, and track id (the cells have been separately tracked for ectoderm, mesoderm, endoderm). We have also included the tracks of the the nucleus channel for sample 1 (this dataframe has x, y, z, t, normalised mezzo expression, and observation id as columns).
a custom Mathematica library for the analysis of tracking data
- follow installation instructions at https://github.com/kthr/Eidomatica
- follow installation instructions at https://github.com/kthr/libEidomatica