Issues

• Visium spots and image mirrored in y after toSpatialFeatureExperiment() from a SpatialExperiment

  pachterlab/SpatialFeatureExperiment#88 · Filter by author CuiweiG opened on Sep 24, 2026

• Improve documentation on coercion from SCE and SPE

  documentation
  pachterlab/SpatialFeatureExperiment#87 · Filter by author lambdamoses opened on May 6, 2026
  

• Load output from other segmentation tools

  pachterlab/SpatialFeatureExperiment#83 · Filter by author PietroD opened on Dec 2, 2025
  3

• Workflow to incorporate H&E image (post-Xenium) info SFE?

  pachterlab/SpatialFeatureExperiment#78 · Filter by author dpcook opened on Jul 30, 2025

• Hack engineering CRS in WKT to use PROJ for affine transformations

  Feature

  pachterlab/SpatialFeatureExperiment#76 · Filter by author lambdamoses opened on Jun 28, 2025

• Find spatial neighborhood graph based on any geometric predicate

  intermediate
  Feature

  pachterlab/SpatialFeatureExperiment#75 · Filter by author lambdamoses opened on Jun 27, 2025

• merge SFE objects

  pachterlab/SpatialFeatureExperiment#69 · Filter by author cathalgking opened on Jun 2, 2025
  2

• Convert units

  enhancementintermediate
  pachterlab/SpatialFeatureExperiment#57 · Filter by author lambdamoses opened on Nov 14, 2024
  3

• Conversion of sfe Object to AnnData

  pachterlab/SpatialFeatureExperiment#56 · Filter by author aasingh2 opened on Nov 14, 2024
  12

• New implementation of affine transformations of SFE objects

  advancedenhancement
  pachterlab/SpatialFeatureExperiment#54 · Filter by author lambdamoses opened on Oct 25, 2024
  1

• make readSpatialxe output from nf-core spatialxe

  advancedenhancement
  pachterlab/SpatialFeatureExperiment#53 · Filter by author alikhuseynov opened on Oct 22, 2024

• make readProseg from proseg segmentation output

  enhancementintermediate
  pachterlab/SpatialFeatureExperiment#52 · Filter by author alikhuseynov opened on Oct 11, 2024

• Optimize VisiumHD loading

  intermediateoptimizationrefactor
  pachterlab/SpatialFeatureExperiment#51 · Filter by author alikhuseynov opened on Oct 6, 2024
  2

• Capacity Error with readXenium() Function and Issues Combining Samples Using cbind()

  pachterlab/SpatialFeatureExperiment#48 · Filter by author aasingh2 opened on Aug 5, 2024
  9

• Could you add a function for plotting a reverse y-axis like GIOTTO? mirror or mirrorImg is not enough. Maybe a Mirror_Y_axis function To facilitate drawing and bridge the gap between different softwares

  pachterlab/SpatialFeatureExperiment#47 · Filter by author huiyijiangling opened on Jul 11, 2024
  1

• add readAkoya

  enhancementintermediate
  pachterlab/SpatialFeatureExperiment#42 · Filter by author alikhuseynov opened on Mar 25, 2024

• Vignette on registering adjacent sections

  documentationenhancementintermediate
  pachterlab/SpatialFeatureExperiment#38 · Filter by author lambdamoses opened on Mar 16, 2024
  

• Better support the complexity in sample relations

  advancedenhancement
  pachterlab/SpatialFeatureExperiment#33 · Filter by author lambdamoses opened on Mar 3, 2024
  4

  

• Use geometry to decide which cells should have sample_id changed

  advancedenhancement
  pachterlab/SpatialFeatureExperiment#31 · Filter by author lambdamoses opened on Feb 21, 2024
  

• Change sample_id with list of cell IDs

  enhancementintermediate
  pachterlab/SpatialFeatureExperiment#30 · Filter by author lambdamoses opened on Feb 21, 2024
  

• Merge method for SFE

  pachterlab/SpatialFeatureExperiment#29 · Filter by author lambdamoses opened on Feb 21, 2024
  3

• Get and set the primary colGeometry

  beginnerenhancement
  pachterlab/SpatialFeatureExperiment#24 · Filter by author lambdamoses opened on Feb 13, 2024
  2

• Allow more than sf class in the Geometries

  advancedenhancement
  pachterlab/SpatialFeatureExperiment#21 · Filter by author lambdamoses opened on Feb 5, 2024
  

• Supporting 3D cell segmentation

  advancedenhancement
  pachterlab/SpatialFeatureExperiment#20 · Filter by author lambdamoses opened on Feb 5, 2024

• Add readMolKart Resolve Bioscience

  enhancementintermediate
  pachterlab/SpatialFeatureExperiment#18 · Filter by author alikhuseynov opened on Dec 7, 2023