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czbiohub-sf / zebrahub_analysis

Analysis of single-cell single-embryo RNA seq data from the zebrafish developmental atlas Zebrahub.
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How did you generate the RNA velocity flow visualization? #1

Closed cyrilcros closed 7 months ago

cyrilcros commented 8 months ago

Hi, would you mind explaining how you generate the "cell flows" based on RNA Velocity data in Supp. Video 6? Was it also done via Napari? I have been using your repo to build 3D UMAPs of my lab's own data, which are quite useful. I have gone through the RNA velocity notebooks, and I see how you use Plotly to generate 3D cones. I was wondering how you got from that to the flow video. Thanks for the great preprint and commitment to open code/open data!

royerloic commented 7 months ago

Hi Cyril, the flow videos were made by a professional graphics designer and paid for. I don't have the code for that unfortunately, but I hope that one day we can design our own system to do that.

cyrilcros commented 7 months ago

Thank you for looking into this, it does look impressive.