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data inputs for visium HD or xenium from other third-party pipeline for segmentation #3

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data inputs for visium HD or xenium from other third-party pipeline for segmentation#3

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@KunHHE
KunHHE
opened on Sep 26, 2025

Hi, @interactivereport thansk for this new tool. Regarding the inputs, looks like the visium HD or xenium are all input from the orginal outputs directly from spaceranger or xeniumranger, then for the downstream all-in-one analysis. my question is, for visium HD or xenium, we always need to do segmentation either using starist or cellpose or othe third=party pipelines, so the data inputs won't be the same to the Ranger outputs, it will be .zarr or h5ad file, for example. So this case, spacesequest cannot process the new outputs any more? Thank you!

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data inputs for visium HD or xenium from other third-party pipeline for segmentation · Issue #3 · interactivereport/SpaceSequest · GitHub
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      data inputs for visium HD or xenium from other third-party pipeline for segmentation #3
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      data inputs for visium HD or xenium from other third-party pipeline for segmentation#3
      Description
      @KunHHE
      KunHHE
      opened on Sep 26, 2025
      Hi, @interactivereport thansk for this new tool. Regarding the inputs, looks like the visium HD or xenium are all input from the orginal outputs directly from spaceranger or xeniumranger, then for the downstream all-in-one analysis. my question is, for visium HD or xenium, we always need to do segmentation either using starist or cellpose or othe third=party pipelines, so the data inputs won't be the same to the Ranger outputs, it will be .zarr or h5ad file, for example. So this case, spacesequest cannot process the new outputs any more? Thank you!
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data inputs for visium HD or xenium from other third-party pipeline for segmentation · Issue #3 · interactivereport/SpaceSequest · GitHub
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          data inputs for visium HD or xenium from other third-party pipeline for segmentation #3
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          data inputs for visium HD or xenium from other third-party pipeline for segmentation#3
          Description
          @KunHHE
          KunHHE
          opened on Sep 26, 2025
          Hi, @interactivereport thansk for this new tool. Regarding the inputs, looks like the visium HD or xenium are all input from the orginal outputs directly from spaceranger or xeniumranger, then for the downstream all-in-one analysis. my question is, for visium HD or xenium, we always need to do segmentation either using starist or cellpose or othe third=party pipelines, so the data inputs won't be the same to the Ranger outputs, it will be .zarr or h5ad file, for example. So this case, spacesequest cannot process the new outputs any more? Thank you!
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data inputs for visium HD or xenium from other third-party pipeline for segmentation · Issue #3 · interactivereport/SpaceSequest · GitHub
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              data inputs for visium HD or xenium from other third-party pipeline for segmentation #3
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              Open
              data inputs for visium HD or xenium from other third-party pipeline for segmentation#3
              Description
              @KunHHE
              KunHHE
              opened on Sep 26, 2025
              Hi, @interactivereport thansk for this new tool. Regarding the inputs, looks like the visium HD or xenium are all input from the orginal outputs directly from spaceranger or xeniumranger, then for the downstream all-in-one analysis. my question is, for visium HD or xenium, we always need to do segmentation either using starist or cellpose or othe third=party pipelines, so the data inputs won't be the same to the Ranger outputs, it will be .zarr or h5ad file, for example. So this case, spacesequest cannot process the new outputs any more? Thank you!
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data inputs for visium HD or xenium from other third-party pipeline for segmentation · Issue #3 · interactivereport/SpaceSequest · GitHub
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                  data inputs for visium HD or xenium from other third-party pipeline for segmentation #3
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                  data inputs for visium HD or xenium from other third-party pipeline for segmentation#3
                  Description
                  @KunHHE
                  KunHHE
                  opened on Sep 26, 2025
                  Hi, @interactivereport thansk for this new tool. Regarding the inputs, looks like the visium HD or xenium are all input from the orginal outputs directly from spaceranger or xeniumranger, then for the downstream all-in-one analysis. my question is, for visium HD or xenium, we always need to do segmentation either using starist or cellpose or othe third=party pipelines, so the data inputs won't be the same to the Ranger outputs, it will be .zarr or h5ad file, for example. So this case, spacesequest cannot process the new outputs any more? Thank you!
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data inputs for visium HD or xenium from other third-party pipeline for segmentation · Issue #3 · interactivereport/SpaceSequest · GitHub
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                      data inputs for visium HD or xenium from other third-party pipeline for segmentation #3
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                      data inputs for visium HD or xenium from other third-party pipeline for segmentation#3
                      Description
                      @KunHHE
                      KunHHE
                      opened on Sep 26, 2025
                      Hi, @interactivereport thansk for this new tool. Regarding the inputs, looks like the visium HD or xenium are all input from the orginal outputs directly from spaceranger or xeniumranger, then for the downstream all-in-one analysis. my question is, for visium HD or xenium, we always need to do segmentation either using starist or cellpose or othe third=party pipelines, so the data inputs won't be the same to the Ranger outputs, it will be .zarr or h5ad file, for example. So this case, spacesequest cannot process the new outputs any more? Thank you!
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data inputs for visium HD or xenium from other third-party pipeline for segmentation · Issue #3 · interactivereport/SpaceSequest · GitHub
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                          data inputs for visium HD or xenium from other third-party pipeline for segmentation #3
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                          data inputs for visium HD or xenium from other third-party pipeline for segmentation#3
                          Description
                          @KunHHE
                          KunHHE
                          opened on Sep 26, 2025
                          Hi, @interactivereport thansk for this new tool. Regarding the inputs, looks like the visium HD or xenium are all input from the orginal outputs directly from spaceranger or xeniumranger, then for the downstream all-in-one analysis. my question is, for visium HD or xenium, we always need to do segmentation either using starist or cellpose or othe third=party pipelines, so the data inputs won't be the same to the Ranger outputs, it will be .zarr or h5ad file, for example. So this case, spacesequest cannot process the new outputs any more? Thank you!
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data inputs for visium HD or xenium from other third-party pipeline for segmentation · Issue #3 · interactivereport/SpaceSequest · GitHub
                              Skip to content
                              data inputs for visium HD or xenium from other third-party pipeline for segmentation #3
                              Open
                              Open
                              data inputs for visium HD or xenium from other third-party pipeline for segmentation#3
                              Description
                              @KunHHE
                              KunHHE
                              opened on Sep 26, 2025
                              Hi, @interactivereport thansk for this new tool. Regarding the inputs, looks like the visium HD or xenium are all input from the orginal outputs directly from spaceranger or xeniumranger, then for the downstream all-in-one analysis. my question is, for visium HD or xenium, we always need to do segmentation either using starist or cellpose or othe third=party pipelines, so the data inputs won't be the same to the Ranger outputs, it will be .zarr or h5ad file, for example. So this case, spacesequest cannot process the new outputs any more? Thank you!
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