Input Data

SpatialTis use AnnData as input format.

ROI Information

If you want to process multiple ROIs at the same time, It’s important that you annotate your cell with ROI.

An example table from AnnData.obs will look like this:

Stage	Patient	Tissue	ROI	Cell_Type
Stage_1	Patient_1	Lung	ROI1	B Cell
Stage_1	Patient_1	Lung	ROI2	T Cell
Stage_2	Patient_3	Breast	ROI3	Tumor
…	…	…	…	…

In this table, the columns Stage, Patient, Tissue and ROI tells the information of ROI. Those information wil be shown in the visualization. The column ROI should assign a unique name for each ROI.

Spatial Coordination

Centroid

SpatialTis accepts different kinds of spatial coordination format.

• (Default) One key in .obsm, it should be a numpy.ndarray, default will read from spatial

• Two/three columns in .obs, each store one dimension of coordination. Respectively, x, y and z if you have 3D data.

• One column in .obs stored as wkt (well-known text) format, which could be easily serialized and deserialized. Or python list/tuple.

If you have two columns X and Y in AnnData.obs that store x, y coordination, you could transform them into wkt format:

>>> import spatialtis as st
>>> st.wkt_points(data, ('X', 'Y'))

Or if you save your coordination in single column centroid, transform it like:

>>> st.wkt_points(data, 'centroid')

Cell Shape (Polygon)

SpatialTis only reads polygons in wkt format, if you don’t have wkt ready format. You should store a polygon in an array container like [(1, 2), (3, 4), ..., (100, 100)]. Store all your polygons in one column. You can now transform it to wkt format:

>>> st.wkt_shapes(data, 'shape')