parhyale_morpho

Codes and data related to parhyale morphogenesis project lead by Beatrice Steinert of the Extavour lab at Harvard University.

Codes related to analysis of the cell shapes and plots resulting from the analysis are contained in the Jupyter notebook BS_CK_Consolidated.ipynb

The BS_CK_Consolidated.pdf is the PDF version of the notebook for those who want to just browse through the code. All the data files needed for the codes to run are also contained in the main directory. So please download all the files and keep them in the same directory as BS_CK_Consolidated.ipynb for the codes to run.

Cellular Potts Model simulation of the parhyale tissue growth

parhyale_hpf26.zip is the zipped Compucell3D project folder. It contains all the relevant files needed to run the Compucell3D simulations. The project was created using Compucell3D Version="4.5.0". Compucell3D is freely available for download at https://compucell3d.org/

Files related to cell tracking

The following files contain cell lineage tracks for three Parhyale hawaiensis embryos (WT1, WT2, WT3) that were imaged on a SiMView multiview lightsheet microscope from 9 to 70-74 hours post fertilization. Cells were tracked using both nuclear and membrane channels with the ImageJ plugins MaMuT (WT1_whole_embryo.xml, WT_03_2018_Er-El-Ep.xml) or Mastodon (WT2_whole_embryo.mastodon). MaMuT tracking files can be easily imported and converted into .mastodon files for further analysis with Mastodon. In the WT1 and WT2 tracking files the 6 lineage trees correspond to the 16-cell stage ectodermal blastomeres: Epl, Epr, Elp, Ela, Erp, and Era.
Opening each file for further cell tracking requires the accompanying .h5 image file and BigDataViewer .xml files, which must be kept together in the same directory. These files can be made available upon request. For further information about how these files were made see the Methods of [bioarchive link / DOI HERE]

• Lightsheet WT1 cell tracks: WT1_whole_embryo.xml
• Lightsheet WT2 cell tracks: WT2_whole_embryo.mastodon
• Lightsheet WT3 cell tracks: WT_03_2018_Er-El-Ep.xml
• Staging table for lightsheet datasets: PH_LIGHTSHEET_DATASET_TIMING-final.csv

Tracking software documentation

• MaMuT : (https://imagej.net/plugins/mamut/)
• Mastodon : (https://imagej.net/plugins/mastodon)

Supplementary Videos

1. SI video 1 : WT1_Movie34_LynGFP-in_9fps.avi
2. SI video 2 : WT1_Movie37_H2BmCherry-in_9fps.avi
3. SI video 3 : 16-cell_domain_stop-motion_animation.mp4
4. SI video 4 : Midline_formation_movie.avi