Different input modes

Depending on your data and preferences, you can use 4 types of inputs. Specifically, it depends on whether (i) you have one or multiple slides and (ii) you prefer to concatenate your data.

Info

In all cases, the data structure is AnnData. We may support MuData in the future.

1. One slide mode

This case is the easiest one. You simply have one AnnData object corresponding to one slide.

You can follow the first section of the main usage tutorial.

2. Multiple slides, one AnnData object

If you have multiple slides with the same gene panel, you can concatenate them into one AnnData object. In that case, make sure you keep a column in adata.obs that denotes which cell corresponds to which slide.

Then, remind this column, and pass it to novae.utils.spatial_neighbors.

Example

For instance, you can do:

novae.utils.spatial_neighbors(adata, slide_key="my-slide-id-column")

3. Multiple slides, one AnnData object per slide

If you have multiple slides, you may prefer to keep one AnnData object for each slide. This is also convenient if you have different gene panels and can't concatenate your data.

That case is pretty easy, since most functions and methods of Novae also support a list of AnnData objects as inputs. Therefore, simply pass a list of AnnData object, as below:

Example

adatas = [adata_1, adata_2, ...]

novae.utils.spatial_neighbors(adatas)

model.compute_representations(adatas, zero_shot=True)

4. Multiple slides, multiple slides per AnnData object

If you have multiple slides and multiple panels, instead of the above option, you could have one AnnData object per panel, and multiple slides inside each AnnData object. In that case, make sure you keep a column in adata.obs that denotes which cell corresponds to which slide.

Then, remind this column, and pass it to novae.utils.spatial_neighbors. The other functions don't need this argument.

Example

For instance, you can do:

adatas = [adata_1, adata_2, ...]

novae.utils.spatial_neighbors(adatas, slide_key="my-slide-id-column")

model.compute_representations(adatas, zero_shot=True)