deepspatial.core.DeepSpatial.reconstruct_full_volume

deepspatial.core.DeepSpatial.reconstruct_full_volume#

DeepSpatial.reconstruct_full_volume(adata_list: list, thickness: float, steps: int = 100, chunk_size: int = 2048, device: str = 'auto') → AnnData[source]#

High-level API to reconstruct the entire 3D volume from a list of slices.

Parameters:

  • adata_list – Ordered list of AnnData slices.

  • thickness – Target physical distance (um) between cells in the Z-axis.

  • steps – Number of ODE integration steps per gap.

  • chunk_size – Processing batch size to prevent OOM on large datasets.

  • device – Target device for the entire reconstruction process.

Returns:

A single merged AnnData object representing the continuous 3D volume.

Contents