Three dimensional reconstruction

Spateo is equipped with sophisticated methods for building 3D spatiotemporal models by aligning serial sections of tissue, organ or embryos across different stages that can be measured by stereo-seq or other high definition spatial transcriptomics technologies. The ability of Spateo to 3D spatiotemporal models enables us to evolve from reductionism of single cells to the holisticism of tissues and organs, heralding a paradigm shift in moving toward studying the ecology of tissue and organ while still offering us the opportunity to reveal associated molecular mechanisms.

Here we will present a series of notebooks that showcase:

1. how we can leverage Spateo to build whole body 3D point-cloud, surface and volume models of drosophila embryo at the E8-10 stage.

2. how we can leverage Spateo to build 3D surface and volume models of each tissue type.

3. how we can leverage Spateo to perform novel morphometric analyses.

4. how we can leverage Spateo to learn continuous expression pattern in the 3D volume model by kernel methods.

5. how we can leverage Spateo to learn continuous expression pattern in the 3D volume model by a new deep learning methods.

• 1.slices alignment
• 2.three dims models reconstruction
• 3.three dims models reconstruction of subpopulations
• 4.morphological features of reconstructed model
• 5.AP&DV axis analysis
• 6.backbone analysis
• Visualize 3D models with spateo
• Animation of 3D models generated by spateo