Rocketeer

Another workaround may be like this: ``` from scipy import ndimage result = ndimage.center_of_mass(masks, masks, np.unique(masks)) resultList = list(result) df = pd.DataFrame( resultList, columns=['row', 'column']) df.drop(0, inplace=True, axis=0) #remove background...

> I encountered the same error too but solved it by filtering those genes with all zero counts. I agree. With `sample 0)` command.

> Hi @VPetukhov I wonder how to plot the cells (in polygon shapes) in the 2D tissue dimension after I finished clustering and cell type annotation. I saw that the...

# Reproduce error `merge R version 4.3.0 (2023-04-21 ucrt) > Platform: x86_64-w64-mingw32/x64 (64-bit) > Running under: Windows 10 x64 (build 18363) > > Matrix products: default > > > locale:...

I resolved this question by changing the type of `seurat_obj@images@slice1@coordinates` from character to int. I could visualize the distribution of gene expression using `SpatialFeaturePlot` now with `image.alpha = 0` because...

I faced the same issue. I'd like to change the BLAST algorithm to `Somewhat similar sequences (blastn)` as shown in BLAST webpage(https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome), so I can show the whole results without...

Answer to myself. `query_blast

You should write `spg.calculate_adj_matrix(x = x_pixel,y = y_pixel, histology=False)`.

Thanks for your reply! - About question 3, is this a plot overlapping an RNA spot distribution plot with a processed DAPI image? - New question about convex hull: I'd...

I recently resolved this error by adding the below code to let the for loop skip processing the empty tiles. ``` for tile_num in range(out.shape[0]): if tile_num == 6 or...