Issues

• CosMx reader: store FOV rectangles in the element metadata so cells can be assigned to FOVs

  saeyslab/harpy#273 · Filter by author ArneDefauw opened on Oct 23, 2026
  

• aggregate_points returns a backed table, while read_zarr and add_table return lazy matrices

  saeyslab/harpy#272 · Filter by author ArneDefauw opened on Oct 23, 2026

• Automatic sharding no longer groups the stored chunks of dense matrices (anndata 0.13)

  saeyslab/harpy#270 · Filter by author ArneDefauw opened on Oct 22, 2026
  2

• Move away from the unmaintained crick dependency to bump to Python 3.14: replace t-digest percentiles with a histogram-based percentile

  saeyslab/harpy#269 · Filter by author ArneDefauw opened on Oct 22, 2026

• Table QC: summarize tables without a SpatialData annotation

  saeyslab/harpy#268 · Filter by author ArneDefauw opened on Oct 21, 2026

• Table QC: per-instance share of a class's points in its top features

  saeyslab/harpy#267 · Filter by author ArneDefauw opened on Oct 20, 2026

• Profile and, where material, reduce the latency of the out-of-core aggregate_points path

  enhancement
  saeyslab/harpy#266 · Filter by author ArneDefauw opened on Oct 19, 2026
  1

• Aggregate points from a precomputed per-transcript cell assignment

  enhancement
  saeyslab/harpy#265 · Filter by author ArneDefauw opened on Oct 10, 2026

• Avoid rewriting the complete .obsm matrix for regional updates

  enhancement
  saeyslab/harpy#263 · Filter by author ArneDefauw opened on Oct 1, 2026
  1

• Visium HD reader does not support segmentation results

  saeyslab/harpy#257 · Filter by author julienmortier opened on Jul 16, 2026
  1

• Xenium: support transcript filtering based on transcript quality value (Q-score)

  saeyslab/harpy#255 · Filter by author SilverViking opened on Jun 29, 2026

• optimize hp.im.merge_labels_nuclei

  enhancement
  saeyslab/harpy#248 · Filter by author ArneDefauw opened on May 25, 2026
  

• output not specified in hp.datasets.xenium_human_ovarian_cancer results in ValueError

  saeyslab/harpy#245 · Filter by author ArneDefauw opened on May 6, 2026

• harpy.im.pixel_clustering_preprocess with scale_factors error

  saeyslab/harpy#243 · Filter by author nbonine opened on May 1, 2026
  2

• Feature Request: Pixels-to-Cell by Agglomerative Pixel Clustering

  saeyslab/harpy#241 · Filter by author DarioS opened on Apr 30, 2026

• Clean Up ProcessTable and Replace Constructor-Side-Effect Validation

  saeyslab/harpy#235 · Filter by author ArneDefauw opened on Apr 17, 2026

• Optimize ProcessTable._get_adata() for .obs-only updates

  saeyslab/harpy#233 · Filter by author ArneDefauw opened on Apr 2, 2026
  1

• allow bins="auto" in hp.qc.image_histogram

  saeyslab/harpy#232 · Filter by author ArneDefauw opened on Apr 1, 2026

• Extend niche analysis methods beyond nhood_kmeans and nhood_lda

  enhancement
  saeyslab/harpy#230 · Filter by author ArneDefauw opened on Mar 31, 2026

• harpy.tb.bin_counts

  enhancementgood first issue
  saeyslab/harpy#227 · Filter by author ArneDefauw opened on Mar 28, 2026

• harpy.im.transcript_density

  enhancementgood first issue
  saeyslab/harpy#226 · Filter by author ArneDefauw opened on Mar 27, 2026

• harpy.pl.plot_transcript_density

  enhancementgood first issue
  saeyslab/harpy#225 · Filter by author ArneDefauw opened on Mar 26, 2026

• Only add valid shapes when calling harpy.sh.add_shapes_layer

  enhancementgood first issue
  saeyslab/harpy#224 · Filter by author ArneDefauw opened on Mar 26, 2026

• add sensible default for coordinates in harpy.tb.add_points_layer

  enhancement
  saeyslab/harpy#223 · Filter by author ArneDefauw opened on Mar 26, 2026

• docs merge labels layers

  documentation
  saeyslab/harpy#193 · Filter by author ArneDefauw opened on Feb 17, 2026