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Best Practice for CCI Analysis on Visium HD Data with Subset Cell Types #347

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Best Practice for CCI Analysis on Visium HD Data with Subset Cell Types#347

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@meisproject
meisproject
opened on Apr 22, 2026

Thank you for developing such an excellent software tool!

I'm currently using stlearn for CCI analysis on Visium HD data, and I'm only interested in a subset of specific cell types.

I have a question about the optimal workflow: Should I filter the AnnData object to retain only my cell types of interest before performing CCI analysis (note that these cell types may not be spatially contiguous), or should I follow the Xenium tutorial approach by performing CCI analysis on all cells after gridding, and then filter for my cell types of interest only during the visualization/plotting stage?

I would greatly appreciate your guidance on the recommended best practice for this scenario.
Thank you in advance for your time and help!

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Best Practice for CCI Analysis on Visium HD Data with Subset Cell Types · Issue #347 · BiomedicalMachineLearning/stLearn · GitHub
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      Best Practice for CCI Analysis on Visium HD Data with Subset Cell Types #347
      Open
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      Best Practice for CCI Analysis on Visium HD Data with Subset Cell Types#347
      Description
      @meisproject
      meisproject
      opened on Apr 22, 2026
      Thank you for developing such an excellent software tool!
      I'm currently using stlearn for CCI analysis on Visium HD data, and I'm only interested in a subset of specific cell types.
      I have a question about the optimal workflow: Should I filter the AnnData object to retain only my cell types of interest before performing CCI analysis (note that these cell types may not be spatially contiguous), or should I follow the Xenium tutorial approach by performing CCI analysis on all cells after gridding, and then filter for my cell types of interest only during the visualization/plotting stage?
      I would greatly appreciate your guidance on the recommended best practice for this scenario.
      
Thank you in advance for your time and help!
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Best Practice for CCI Analysis on Visium HD Data with Subset Cell Types · Issue #347 · BiomedicalMachineLearning/stLearn · GitHub
          Skip to content
          Best Practice for CCI Analysis on Visium HD Data with Subset Cell Types #347
          Open
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          Best Practice for CCI Analysis on Visium HD Data with Subset Cell Types#347
          Description
          @meisproject
          meisproject
          opened on Apr 22, 2026
          Thank you for developing such an excellent software tool!
          I'm currently using stlearn for CCI analysis on Visium HD data, and I'm only interested in a subset of specific cell types.
          I have a question about the optimal workflow: Should I filter the AnnData object to retain only my cell types of interest before performing CCI analysis (note that these cell types may not be spatially contiguous), or should I follow the Xenium tutorial approach by performing CCI analysis on all cells after gridding, and then filter for my cell types of interest only during the visualization/plotting stage?
          I would greatly appreciate your guidance on the recommended best practice for this scenario.
          
Thank you in advance for your time and help!
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Best Practice for CCI Analysis on Visium HD Data with Subset Cell Types · Issue #347 · BiomedicalMachineLearning/stLearn · GitHub
              Skip to content
              Best Practice for CCI Analysis on Visium HD Data with Subset Cell Types #347
              Open
              Open
              Best Practice for CCI Analysis on Visium HD Data with Subset Cell Types#347
              Description
              @meisproject
              meisproject
              opened on Apr 22, 2026
              Thank you for developing such an excellent software tool!
              I'm currently using stlearn for CCI analysis on Visium HD data, and I'm only interested in a subset of specific cell types.
              I have a question about the optimal workflow: Should I filter the AnnData object to retain only my cell types of interest before performing CCI analysis (note that these cell types may not be spatially contiguous), or should I follow the Xenium tutorial approach by performing CCI analysis on all cells after gridding, and then filter for my cell types of interest only during the visualization/plotting stage?
              I would greatly appreciate your guidance on the recommended best practice for this scenario.
              
Thank you in advance for your time and help!
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Best Practice for CCI Analysis on Visium HD Data with Subset Cell Types · Issue #347 · BiomedicalMachineLearning/stLearn · GitHub
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                  Best Practice for CCI Analysis on Visium HD Data with Subset Cell Types #347
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                  Best Practice for CCI Analysis on Visium HD Data with Subset Cell Types#347
                  Description
                  @meisproject
                  meisproject
                  opened on Apr 22, 2026
                  Thank you for developing such an excellent software tool!
                  I'm currently using stlearn for CCI analysis on Visium HD data, and I'm only interested in a subset of specific cell types.
                  I have a question about the optimal workflow: Should I filter the AnnData object to retain only my cell types of interest before performing CCI analysis (note that these cell types may not be spatially contiguous), or should I follow the Xenium tutorial approach by performing CCI analysis on all cells after gridding, and then filter for my cell types of interest only during the visualization/plotting stage?
                  I would greatly appreciate your guidance on the recommended best practice for this scenario.
                  
Thank you in advance for your time and help!
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Best Practice for CCI Analysis on Visium HD Data with Subset Cell Types · Issue #347 · BiomedicalMachineLearning/stLearn · GitHub
                      Skip to content
                      Best Practice for CCI Analysis on Visium HD Data with Subset Cell Types #347
                      Open
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                      Best Practice for CCI Analysis on Visium HD Data with Subset Cell Types#347
                      Description
                      @meisproject
                      meisproject
                      opened on Apr 22, 2026
                      Thank you for developing such an excellent software tool!
                      I'm currently using stlearn for CCI analysis on Visium HD data, and I'm only interested in a subset of specific cell types.
                      I have a question about the optimal workflow: Should I filter the AnnData object to retain only my cell types of interest before performing CCI analysis (note that these cell types may not be spatially contiguous), or should I follow the Xenium tutorial approach by performing CCI analysis on all cells after gridding, and then filter for my cell types of interest only during the visualization/plotting stage?
                      I would greatly appreciate your guidance on the recommended best practice for this scenario.
                      
Thank you in advance for your time and help!
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Best Practice for CCI Analysis on Visium HD Data with Subset Cell Types · Issue #347 · BiomedicalMachineLearning/stLearn · GitHub
                          Skip to content
                          Best Practice for CCI Analysis on Visium HD Data with Subset Cell Types #347
                          Open
                          Open
                          Best Practice for CCI Analysis on Visium HD Data with Subset Cell Types#347
                          Description
                          @meisproject
                          meisproject
                          opened on Apr 22, 2026
                          Thank you for developing such an excellent software tool!
                          I'm currently using stlearn for CCI analysis on Visium HD data, and I'm only interested in a subset of specific cell types.
                          I have a question about the optimal workflow: Should I filter the AnnData object to retain only my cell types of interest before performing CCI analysis (note that these cell types may not be spatially contiguous), or should I follow the Xenium tutorial approach by performing CCI analysis on all cells after gridding, and then filter for my cell types of interest only during the visualization/plotting stage?
                          I would greatly appreciate your guidance on the recommended best practice for this scenario.
                          
Thank you in advance for your time and help!
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Best Practice for CCI Analysis on Visium HD Data with Subset Cell Types · Issue #347 · BiomedicalMachineLearning/stLearn · GitHub
                              Skip to content
                              Best Practice for CCI Analysis on Visium HD Data with Subset Cell Types #347
                              Open
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                              Best Practice for CCI Analysis on Visium HD Data with Subset Cell Types#347
                              Description
                              @meisproject
                              meisproject
                              opened on Apr 22, 2026
                              Thank you for developing such an excellent software tool!
                              I'm currently using stlearn for CCI analysis on Visium HD data, and I'm only interested in a subset of specific cell types.
                              I have a question about the optimal workflow: Should I filter the AnnData object to retain only my cell types of interest before performing CCI analysis (note that these cell types may not be spatially contiguous), or should I follow the Xenium tutorial approach by performing CCI analysis on all cells after gridding, and then filter for my cell types of interest only during the visualization/plotting stage?
                              I would greatly appreciate your guidance on the recommended best practice for this scenario.
                              
Thank you in advance for your time and help!
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