Ajit Johnson Nirmal

Generally, this is inherently considered during the phenotyping process. The principle is that true B cells typically should exhibit higher CD20 expression than any spillover marker. Are you encountering difficulties...

This step is typically quite manual. I usually analyze the cellular composition of each neighborhood and overlay the data onto the image to assign meaningful names. For instance, a neighborhood...

Hi @PietroD -- I see two potential issues: Please ensure that the XY coordinates are in a global reference frame. It appears that segmentation may have been performed separately for...

First, to correct the scaling issue, you need to convert the X and Y coordinates back to pixel units. If you originally used a resolution factor (e.g., microns per pixel)...

hi @Yuchen588 are these two datasets processed independently and merged by some means into a single `anndata` object? If so at step was it merged?

well, that all sounds appropriate. can you share the code that you used to generate the neighborhoods and subsequent clustering? It is weird that you will get NA's. Just to...

can you try: ``` ### Run the LDA tool adata = sm.tl.spatial_lda(adata, method='knn', knn=10, label='spatial_lda', phenotype='cell.anno') ### Perform spatial clustering adata = sm.tl.spatial_cluster(adata, random_state=0, df_name='spatial_lda', method='kmeans', k=10, label='spatial_lda_kmeans.10.final') ```

hi @ConstensouxAlexis Thank you for raising the bug. Could you update the package `pip install scimap --upgrade` and check if the issue persists? Thank you.

No problem. I have released a new version with the requirements relaxed. Hope it helps.

Hi, I don't think I fully understand your question. Generally, the first column represents the cells to be classified, and the second column indicates the category they should be classified...