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I'm creating 3D tours of open single cell RNA-seq data in UMAP space. Here, using data from 50k brain cells by the allen institute . ( The UMAP position and class of every cell is read into Blender, realized as a stylized, class-specific model I sculpted

Brad Krajina

1,782 subscribers

48,138 次观看 • 3 年前 •via X (Twitter)

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Brad Krajina 的头像

Brad Krajina3 年前

Relevant to the dataset used to produce this video are the following papers from researchers at the @AllenInstitute : I did not contribute to the original seq data, and I am grateful to the researchers for making it open

Brad Krajina 的头像

Brad Krajina3 年前

After projecting the RNA-seq data from the Allen Brain Map into 3D UMAP space using Seurat, reading the UMAP data into Blender was achieved using a csv importer add-on from @smonbrogg

Brad Krajina 的头像

Brad Krajina3 年前

Rendering all of the 3D models without overfilling GPU memory was possible using LOD and camera culling nodes from @erindale_xyz in the Erindale Toolkit- Advanced Geometry Nodes Groups.

Brad Krajina 的头像

Brad Krajina3 年前

Thanks to @CgFigures for a great tutorial on importing csv data into geometry nodes in Blender

Chanchal Kumar 的头像

Chanchal Kumar3 年前

@AllenInstitute Amazing work!!

Brad Krajina 的头像

Brad Krajina3 年前

@AllenInstitute Thanks so much!

Nader 的头像

Nader3 年前

@AllenInstitute Wow, what an incredible endeavor! Thanks for sharing!

Amy Robinson Sterling 的头像

Amy Robinson Sterling3 年前

@AllenInstitute Also I really like the shaders and how you made the nucleus glow

Christopher Akiki 的头像

Christopher Akiki3 年前

@AllenInstitute This is next level 🤯

Zafer Kosar 的头像

Zafer Kosar3 年前

@AllenInstitute Astonishing work

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Select your cell: I'm prototyping an interactive sc RNA-seq portal where the UMAP is dynamically linked to morphing 3D artistic renders of each cell type. You can play with the initial build below.

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A detailed map of mouse brain cell structure and connections, offering insights into how they relate to activity in the mouse brain, is revealed in a package of papers from MICrONS consortium in nature & Nature Methods: Allen Institute naturePortfolio

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199,711 次观看 • 2 年前

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