[Help please] Integrate multiple spatial transcriptomics datasets is not working!

[MatteoRiva95]

Hello everyone,

I am trying to follow this tutorial page:

https://stlearn.readthedocs.io/en/latest/tutorials/Integration_multiple_datasets.html

But when I plot the adata_concat, it returns this image:

Something is wrong: as you can see, the right image is decentrated. I suppose this command from the tutorial is the issue:

adata_concat.obs.loc[adata_concat.obs.batch == "1","imagecol"] = adata_concat.obs.loc[adata_concat.obs.batch == "1","imagecol"].values + 2000

How can I be sure that 2000 is fine and not 3000? What number should I use for my dataset then? How can I be certain that it is right for my spatial dataset?

Can you help me please? Thank you so much in advance!

[MatteoRiva95]

UPDATE:

In order to partially solve the previous issue, I tried not to use the images of the tissue:

block_1 = st.create_stlearn(count=count_matrix_1,spatial=spatial_1,library_id="OSR_IBD_1_A1", scale=1,background_color="white")
block_2 = st.create_stlearn(count=count_matrix_2,spatial=spatial_2,library_id="OSR_IBD_2_B2", scale=1,background_color="white")

adata_concat = block_1.concatenate(block_2)

But if I try to plot a gene with these commands:

plot = st.pl.gene_plot(adata_concat, gene_symbols="MMP3", size = 7.0)
plt.show(plot)

It returns this error:

plot = st.pl.gene_plot(adata_concat, gene_symbols="MMP3", size = 7.0)
Traceback (most recent call last):
File "", line 1, in
File "/home/mriva/.conda/envs/stlearn/lib/python3.8/site-packages/stlearn/plotting/gene_plot.py", line 73, in gene_plot
GenePlot(
File "/home/mriva/.conda/envs/stlearn/lib/python3.8/site-packages/stlearn/plotting/classes.py", line 273, in init
super().init(
File "/home/mriva/.conda/envs/stlearn/lib/python3.8/site-packages/stlearn/plotting/classes.py", line 62, in init
super().init(
File "/home/mriva/.conda/envs/stlearn/lib/python3.8/site-packages/stlearn/classes.py", line 44, in init
self.spot_size = _check_spot_size(self.spatial_data, spot_size)
File "/home/mriva/.conda/envs/stlearn/lib/python3.8/site-packages/stlearn/utils.py", line 41, in _check_spot_size
raise ValueError(
ValueError: When .uns['spatial'][library_id] does not exist, spot_size must be provided directly.