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Removed invert keyword breaks segmentation with cellpose>=4.2

Status: Open.

#259 In saeyslab/harpy;

· lucas-diedrich opened on Aug 5, 2026

Visium HD reader: KeyError: 'global' when reading images

Status: Open.

#258 In saeyslab/harpy;

· julienmortier opened on Jul 16, 2026

Visium HD reader does not support segmentation results

Status: Open.

#257 In saeyslab/harpy;

· julienmortier opened on Jul 16, 2026

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

Status: Open.

#255 In saeyslab/harpy;

· SilverViking opened on Jun 29, 2026

optimize hp.im.merge_labels_nuclei

enhancementNew feature or requestNew feature or request

Status: Open.

#248 In saeyslab/harpy;

· ArneDefauw opened on May 25, 2026

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

Status: Open.

#245 In saeyslab/harpy;

· ArneDefauw opened on May 6, 2026

harpy.im.pixel_clustering_preprocess with scale_factors error

Status: Open.

#243 In saeyslab/harpy;

· nbonine opened on May 1, 2026

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

Status: Open.

#241 In saeyslab/harpy;

· DarioS opened on Apr 30, 2026

Clean Up ProcessTable and Replace Constructor-Side-Effect Validation

Status: Open.

#235 In saeyslab/harpy;

· ArneDefauw opened on Apr 17, 2026

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

Status: Open.

#233 In saeyslab/harpy;

· ArneDefauw opened on Apr 2, 2026

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

Status: Open.

#232 In saeyslab/harpy;

· ArneDefauw opened on Apr 1, 2026

Extend niche analysis methods beyond nhood_kmeans and nhood_lda

enhancementNew feature or requestNew feature or request

Status: Open.

#230 In saeyslab/harpy;

· ArneDefauw opened on Mar 31, 2026