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Output spatially ordered anndata object #1145

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Output spatially ordered anndata object#1145

Description

@ilan-gold
ilan-gold
opened on Jun 17, 2026

Is your feature request related to a problem? Please describe.
I am not 100% certain if this request is supported from the parquet side for shape/points (only going based on https://spatialdata.scverse.org/en/stable/api/SpatialData.html#spatialdata.SpatialData.write) but I'm following up on https://scverse.zulipchat.com/#narrow/channel/315824-spatial/topic/dataloaders.20for.20spatial.20omics/near/591781853

Describe the solution you'd like
I want the anndata object to be ordered by some form of spatial coherence - I can think of two versions:

  1. A pure-spatial approach that relies on some form of quad-tree to do the partitioning and the data would be written in some ordering (C? morton?) of the spatial coordinates of each 4-element leaf node of the tree.
  2. A user-defined neighborhood approach that outputs an approximate ordering so that neighbors are near one-another according to a user-defined neighborhood graph

Describe alternatives you've considered
For the second option, we could upstream this into anndata theoretically or factor out the "generate the linearized in-memory ordering of the indices" part to be reusable. This might actually make more sense TBH but it's not immediately clear to me if there will be a large benefit of the second over the first aside from the fact that the second would be more generalizable to other use-cases outside of spatial data, at the downside of requiring a (spatial) graph to be formed (which requires some form of computation?).

Additional context
The need here is produce data whose ordering is amenable to fast data loading via "batched fetching" i.e., ensuring as many data points as possible (for performance reasons) are contiguous on-disk.

I am not super familiar with spatial workflows so perhaps one makes more sense than the other in a normal pipeline, but I basically suspect we will end up implementing both TBH.

cc @ori-kron-wis@timtreis

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Output spatially ordered `anndata` object · Issue #1145 · scverse/spatialdata · GitHub
      Skip to content
      Output spatially ordered anndata object #1145
      Open
      Open
      Output spatially ordered anndata object#1145
      Description
      @ilan-gold
      ilan-gold
      opened on Jun 17, 2026
      Is your feature request related to a problem? Please describe.
      
I am not 100% certain if this request is supported from the parquet side for shape/points (only going based on https://spatialdata.scverse.org/en/stable/api/SpatialData.html#spatialdata.SpatialData.write) but I'm following up on https://scverse.zulipchat.com/#narrow/channel/315824-spatial/topic/dataloaders.20for.20spatial.20omics/near/591781853
      Describe the solution you'd like
      
I want the anndata object to be ordered by some form of spatial coherence - I can think of two versions:
      1. A pure-spatial approach that relies on some form of quad-tree to do the partitioning and the data would be written in some ordering (C? morton?) of the spatial coordinates of each 4-element leaf node of the tree.
      2. A user-defined neighborhood approach that outputs an approximate ordering so that neighbors are near one-another according to a user-defined neighborhood graph
      Describe alternatives you've considered
      
For the second option, we could upstream this into anndata theoretically or factor out the "generate the linearized in-memory ordering of the indices" part to be reusable. This might actually make more sense TBH but it's not immediately clear to me if there will be a large benefit of the second over the first aside from the fact that the second would be more generalizable to other use-cases outside of spatial data, at the downside of requiring a (spatial) graph to be formed (which requires some form of computation?).
      Additional context
      
The need here is produce data whose ordering is amenable to fast data loading via "batched fetching" i.e., ensuring as many data points as possible (for performance reasons) are contiguous on-disk.
      I am not super familiar with spatial workflows so perhaps one makes more sense than the other in a normal pipeline, but I basically suspect we will end up implementing both TBH.
      cc @ori-kron-wis@timtreis
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Output spatially ordered `anndata` object · Issue #1145 · scverse/spatialdata · GitHub
          Skip to content
          Output spatially ordered anndata object #1145
          Open
          Open
          Output spatially ordered anndata object#1145
          Description
          @ilan-gold
          ilan-gold
          opened on Jun 17, 2026
          Is your feature request related to a problem? Please describe.
          
I am not 100% certain if this request is supported from the parquet side for shape/points (only going based on https://spatialdata.scverse.org/en/stable/api/SpatialData.html#spatialdata.SpatialData.write) but I'm following up on https://scverse.zulipchat.com/#narrow/channel/315824-spatial/topic/dataloaders.20for.20spatial.20omics/near/591781853
          Describe the solution you'd like
          
I want the anndata object to be ordered by some form of spatial coherence - I can think of two versions:
          1. A pure-spatial approach that relies on some form of quad-tree to do the partitioning and the data would be written in some ordering (C? morton?) of the spatial coordinates of each 4-element leaf node of the tree.
          2. A user-defined neighborhood approach that outputs an approximate ordering so that neighbors are near one-another according to a user-defined neighborhood graph
          Describe alternatives you've considered
          
For the second option, we could upstream this into anndata theoretically or factor out the "generate the linearized in-memory ordering of the indices" part to be reusable. This might actually make more sense TBH but it's not immediately clear to me if there will be a large benefit of the second over the first aside from the fact that the second would be more generalizable to other use-cases outside of spatial data, at the downside of requiring a (spatial) graph to be formed (which requires some form of computation?).
          Additional context
          
The need here is produce data whose ordering is amenable to fast data loading via "batched fetching" i.e., ensuring as many data points as possible (for performance reasons) are contiguous on-disk.
          I am not super familiar with spatial workflows so perhaps one makes more sense than the other in a normal pipeline, but I basically suspect we will end up implementing both TBH.
          cc @ori-kron-wis@timtreis
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Output spatially ordered `anndata` object · Issue #1145 · scverse/spatialdata · GitHub
              Skip to content
              Output spatially ordered anndata object #1145
              Open
              Open
              Output spatially ordered anndata object#1145
              Description
              @ilan-gold
              ilan-gold
              opened on Jun 17, 2026
              Is your feature request related to a problem? Please describe.
              
I am not 100% certain if this request is supported from the parquet side for shape/points (only going based on https://spatialdata.scverse.org/en/stable/api/SpatialData.html#spatialdata.SpatialData.write) but I'm following up on https://scverse.zulipchat.com/#narrow/channel/315824-spatial/topic/dataloaders.20for.20spatial.20omics/near/591781853
              Describe the solution you'd like
              
I want the anndata object to be ordered by some form of spatial coherence - I can think of two versions:
              1. A pure-spatial approach that relies on some form of quad-tree to do the partitioning and the data would be written in some ordering (C? morton?) of the spatial coordinates of each 4-element leaf node of the tree.
              2. A user-defined neighborhood approach that outputs an approximate ordering so that neighbors are near one-another according to a user-defined neighborhood graph
              Describe alternatives you've considered
              
For the second option, we could upstream this into anndata theoretically or factor out the "generate the linearized in-memory ordering of the indices" part to be reusable. This might actually make more sense TBH but it's not immediately clear to me if there will be a large benefit of the second over the first aside from the fact that the second would be more generalizable to other use-cases outside of spatial data, at the downside of requiring a (spatial) graph to be formed (which requires some form of computation?).
              Additional context
              
The need here is produce data whose ordering is amenable to fast data loading via "batched fetching" i.e., ensuring as many data points as possible (for performance reasons) are contiguous on-disk.
              I am not super familiar with spatial workflows so perhaps one makes more sense than the other in a normal pipeline, but I basically suspect we will end up implementing both TBH.
              cc @ori-kron-wis@timtreis
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Output spatially ordered `anndata` object · Issue #1145 · scverse/spatialdata · GitHub
                  Skip to content
                  Output spatially ordered anndata object #1145
                  Open
                  Open
                  Output spatially ordered anndata object#1145
                  Description
                  @ilan-gold
                  ilan-gold
                  opened on Jun 17, 2026
                  Is your feature request related to a problem? Please describe.
                  
I am not 100% certain if this request is supported from the parquet side for shape/points (only going based on https://spatialdata.scverse.org/en/stable/api/SpatialData.html#spatialdata.SpatialData.write) but I'm following up on https://scverse.zulipchat.com/#narrow/channel/315824-spatial/topic/dataloaders.20for.20spatial.20omics/near/591781853
                  Describe the solution you'd like
                  
I want the anndata object to be ordered by some form of spatial coherence - I can think of two versions:
                  1. A pure-spatial approach that relies on some form of quad-tree to do the partitioning and the data would be written in some ordering (C? morton?) of the spatial coordinates of each 4-element leaf node of the tree.
                  2. A user-defined neighborhood approach that outputs an approximate ordering so that neighbors are near one-another according to a user-defined neighborhood graph
                  Describe alternatives you've considered
                  
For the second option, we could upstream this into anndata theoretically or factor out the "generate the linearized in-memory ordering of the indices" part to be reusable. This might actually make more sense TBH but it's not immediately clear to me if there will be a large benefit of the second over the first aside from the fact that the second would be more generalizable to other use-cases outside of spatial data, at the downside of requiring a (spatial) graph to be formed (which requires some form of computation?).
                  Additional context
                  
The need here is produce data whose ordering is amenable to fast data loading via "batched fetching" i.e., ensuring as many data points as possible (for performance reasons) are contiguous on-disk.
                  I am not super familiar with spatial workflows so perhaps one makes more sense than the other in a normal pipeline, but I basically suspect we will end up implementing both TBH.
                  cc @ori-kron-wis@timtreis
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var __m = "*";
var __re = new RegExp('^' + ".*" + '
Output spatially ordered `anndata` object · Issue #1145 · scverse/spatialdata · GitHub
                      Skip to content
                      Output spatially ordered anndata object #1145
                      Open
                      Open
                      Output spatially ordered anndata object#1145
                      Description
                      @ilan-gold
                      ilan-gold
                      opened on Jun 17, 2026
                      Is your feature request related to a problem? Please describe.
                      
I am not 100% certain if this request is supported from the parquet side for shape/points (only going based on https://spatialdata.scverse.org/en/stable/api/SpatialData.html#spatialdata.SpatialData.write) but I'm following up on https://scverse.zulipchat.com/#narrow/channel/315824-spatial/topic/dataloaders.20for.20spatial.20omics/near/591781853
                      Describe the solution you'd like
                      
I want the anndata object to be ordered by some form of spatial coherence - I can think of two versions:
                      1. A pure-spatial approach that relies on some form of quad-tree to do the partitioning and the data would be written in some ordering (C? morton?) of the spatial coordinates of each 4-element leaf node of the tree.
                      2. A user-defined neighborhood approach that outputs an approximate ordering so that neighbors are near one-another according to a user-defined neighborhood graph
                      Describe alternatives you've considered
                      
For the second option, we could upstream this into anndata theoretically or factor out the "generate the linearized in-memory ordering of the indices" part to be reusable. This might actually make more sense TBH but it's not immediately clear to me if there will be a large benefit of the second over the first aside from the fact that the second would be more generalizable to other use-cases outside of spatial data, at the downside of requiring a (spatial) graph to be formed (which requires some form of computation?).
                      Additional context
                      
The need here is produce data whose ordering is amenable to fast data loading via "batched fetching" i.e., ensuring as many data points as possible (for performance reasons) are contiguous on-disk.
                      I am not super familiar with spatial workflows so perhaps one makes more sense than the other in a normal pipeline, but I basically suspect we will end up implementing both TBH.
                      cc @ori-kron-wis@timtreis
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Output spatially ordered `anndata` object · Issue #1145 · scverse/spatialdata · GitHub
                          Skip to content
                          Output spatially ordered anndata object #1145
                          Open
                          Open
                          Output spatially ordered anndata object#1145
                          Description
                          @ilan-gold
                          ilan-gold
                          opened on Jun 17, 2026
                          Is your feature request related to a problem? Please describe.
                          
I am not 100% certain if this request is supported from the parquet side for shape/points (only going based on https://spatialdata.scverse.org/en/stable/api/SpatialData.html#spatialdata.SpatialData.write) but I'm following up on https://scverse.zulipchat.com/#narrow/channel/315824-spatial/topic/dataloaders.20for.20spatial.20omics/near/591781853
                          Describe the solution you'd like
                          
I want the anndata object to be ordered by some form of spatial coherence - I can think of two versions:
                          1. A pure-spatial approach that relies on some form of quad-tree to do the partitioning and the data would be written in some ordering (C? morton?) of the spatial coordinates of each 4-element leaf node of the tree.
                          2. A user-defined neighborhood approach that outputs an approximate ordering so that neighbors are near one-another according to a user-defined neighborhood graph
                          Describe alternatives you've considered
                          
For the second option, we could upstream this into anndata theoretically or factor out the "generate the linearized in-memory ordering of the indices" part to be reusable. This might actually make more sense TBH but it's not immediately clear to me if there will be a large benefit of the second over the first aside from the fact that the second would be more generalizable to other use-cases outside of spatial data, at the downside of requiring a (spatial) graph to be formed (which requires some form of computation?).
                          Additional context
                          
The need here is produce data whose ordering is amenable to fast data loading via "batched fetching" i.e., ensuring as many data points as possible (for performance reasons) are contiguous on-disk.
                          I am not super familiar with spatial workflows so perhaps one makes more sense than the other in a normal pipeline, but I basically suspect we will end up implementing both TBH.
                          cc @ori-kron-wis@timtreis
                          Metadata
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Output spatially ordered `anndata` object · Issue #1145 · scverse/spatialdata · GitHub
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                              Output spatially ordered anndata object #1145
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                              Output spatially ordered anndata object#1145
                              Description
                              @ilan-gold
                              ilan-gold
                              opened on Jun 17, 2026
                              Is your feature request related to a problem? Please describe.
                              
I am not 100% certain if this request is supported from the parquet side for shape/points (only going based on https://spatialdata.scverse.org/en/stable/api/SpatialData.html#spatialdata.SpatialData.write) but I'm following up on https://scverse.zulipchat.com/#narrow/channel/315824-spatial/topic/dataloaders.20for.20spatial.20omics/near/591781853
                              Describe the solution you'd like
                              
I want the anndata object to be ordered by some form of spatial coherence - I can think of two versions:
                              1. A pure-spatial approach that relies on some form of quad-tree to do the partitioning and the data would be written in some ordering (C? morton?) of the spatial coordinates of each 4-element leaf node of the tree.
                              2. A user-defined neighborhood approach that outputs an approximate ordering so that neighbors are near one-another according to a user-defined neighborhood graph
                              Describe alternatives you've considered
                              
For the second option, we could upstream this into anndata theoretically or factor out the "generate the linearized in-memory ordering of the indices" part to be reusable. This might actually make more sense TBH but it's not immediately clear to me if there will be a large benefit of the second over the first aside from the fact that the second would be more generalizable to other use-cases outside of spatial data, at the downside of requiring a (spatial) graph to be formed (which requires some form of computation?).
                              Additional context
                              
The need here is produce data whose ordering is amenable to fast data loading via "batched fetching" i.e., ensuring as many data points as possible (for performance reasons) are contiguous on-disk.
                              I am not super familiar with spatial workflows so perhaps one makes more sense than the other in a normal pipeline, but I basically suspect we will end up implementing both TBH.
                              cc @ori-kron-wis@timtreis
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