I want to reconstruct a 3D for my data from MERFISH experiments. I did cell segmentation and downstream analysis. I got the adata from scanpy for each slice. I found the input files are different from the STIM. I want to know could STIM be used for h5ad file from scanpy.
When I tried the st-explorer -i my .h5ad, there are the warning:
[2025-08-14T10:05:15,657] [main] WARN : Could not read column names from /obs
[2025-08-14T10:05:15,659] [main] WARN : Could not read column names from /var
When I select one gene:
[2025-08-14T10:05:31,218] [Thread-1] INFO : rendering gene: tbx1 of slide: STData, #dim: 2, #genes: 133, #locations: 594
Interval: [612.296506382054, 3249.110205468772] -> [1129.792448474931, 3782.4082840714223], size (517.495942092877, 533.2980786026501)
RenderInterval: [612.0, 3249.0] -> [1130.0, 3783.0], size (518.0, 534.0)
I want to reconstruct a 3D for my data from MERFISH experiments. I did cell segmentation and downstream analysis. I got the adata from scanpy for each slice. I found the input files are different from the STIM. I want to know could STIM be used for h5ad file from scanpy.
When I tried the st-explorer -i my .h5ad, there are the warning:
[2025-08-14T10:05:15,657] [main] WARN : Could not read column names from /obs
[2025-08-14T10:05:15,659] [main] WARN : Could not read column names from /var
When I select one gene:
[2025-08-14T10:05:31,218] [Thread-1] INFO : rendering gene: tbx1 of slide: STData, #dim: 2, #genes: 133, #locations: 594
Interval: [612.296506382054, 3249.110205468772] -> [1129.792448474931, 3782.4082840714223], size (517.495942092877, 533.2980786026501)
RenderInterval: [612.0, 3249.0] -> [1130.0, 3783.0], size (518.0, 534.0)