saeyslab/harpy

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Single-cell spatial omics analysis that makes you happy!

Stars: 75
Forks: 7
Open beginner issues: 6
Indexed issues: 28
Avg merge: 2m
Merged PRs (30d): 1

Dominant language: Python
License: No license data
Last GitHub push: Sep 10, 2026
Latest indexed: Sep 20, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: good first issue

Beginner friendly Everything

Open All

28 open issues indexed

Removed `invert` keyword breaks segmentation with cellpose>=4.2 Open

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

saeyslab/harpy#259 · 1 comment · 1 reaction · Opened Aug 5, 2026
Visium HD reader: KeyError: 'global' when reading images Open

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

saeyslab/harpy#258 · Opened Jul 16, 2026
Visium HD reader does not support segmentation results Open

Difficulty 3/5 1-2 days Newbie friendliness 58/100

saeyslab/harpy#257 · 1 comment · Opened Jul 16, 2026
Xenium: support transcript filtering based on transcript quality value (Q-score) Open

Difficulty 3/5 1-2 days Newbie friendliness 68/100

saeyslab/harpy#255 · Opened Jun 29, 2026
optimize hp.im.merge_labels_nuclei Open

enhancement

saeyslab/harpy#248 · 1 assignee · Opened May 25, 2026
output not specified in hp.datasets.xenium_human_ovarian_cancer results in ValueError Open

Difficulty 2/5 1-3 hours Newbie friendliness 62/100

saeyslab/harpy#245 · Opened May 6, 2026
harpy.im.pixel_clustering_preprocess with scale_factors error Open

Difficulty 3/5 1-2 days Newbie friendliness 55/100

saeyslab/harpy#243 · 2 comments · Opened May 1, 2026
Feature Request: Pixels-to-Cell by Agglomerative Pixel Clustering Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

saeyslab/harpy#241 · Opened Apr 30, 2026
Clean Up `ProcessTable` and Replace Constructor-Side-Effect Validation Open

Difficulty 5/5 Over a week Newbie friendliness 42/100

saeyslab/harpy#235 · Opened Apr 17, 2026
Optimize ProcessTable._get_adata() for .obs-only updates Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

saeyslab/harpy#233 · 1 comment · Opened Apr 2, 2026
allow bins="auto" in hp.qc.image_histogram Open

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

saeyslab/harpy#232 · Opened Apr 1, 2026
Extend niche analysis methods beyond `nhood_kmeans` and `nhood_lda` Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

saeyslab/harpy#230 · Opened Mar 31, 2026
harpy.tb.bin_counts Open

enhancement good first issue

Difficulty 5/5 Over a week Newbie friendliness 35/100

saeyslab/harpy#227 · Opened Mar 28, 2026
harpy.im.transcript_density Open

enhancement good first issue

Difficulty 4/5 3-5 days Newbie friendliness 48/100

saeyslab/harpy#226 · Opened Mar 27, 2026
harpy.pl.plot_transcript_density Open

enhancement good first issue

Difficulty 3/5 1-2 days Newbie friendliness 52/100

saeyslab/harpy#225 · Opened Mar 26, 2026
Only add valid shapes when calling harpy.sh.add_shapes_layer Open

enhancement good first issue

Difficulty 3/5 1-2 days Newbie friendliness 63/100

saeyslab/harpy#224 · Opened Mar 26, 2026
add sensible default for coordinates in harpy.tb.add_points_layer Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

saeyslab/harpy#223 · Opened Mar 26, 2026
docs merge labels layers Open

documentation

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

saeyslab/harpy#193 · Opened Feb 17, 2026
Documentation error harpy.im.rasterize Open

documentation

Difficulty 1/5 Under an hour Newbie friendliness 55/100

saeyslab/harpy#179 · Opened Jan 6, 2026
xenium PyArrow OSError: Unexpected end of stream Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 35/100

saeyslab/harpy#168 · 6 comments · 1 reaction · Opened Nov 25, 2025
Quality Control Chapter Lacks Interpretations Open

Difficulty 2/5 1-3 hours Newbie friendliness 65/100

saeyslab/harpy#142 · Opened Jul 10, 2025
Add 'channel_names' argument in 'snr_ratio' definition. Open

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

saeyslab/harpy#134 · Opened May 8, 2025
Error on invalid marker names in a SpatialData object Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

saeyslab/harpy#119 · Opened Apr 2, 2025
Improve documentation of progress bars Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

saeyslab/harpy#111 · Opened Mar 27, 2025
Improve documentation Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

saeyslab/harpy#106 · Opened Mar 26, 2025
Document import/export from QuPath Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

saeyslab/harpy#72 · Opened Nov 20, 2024
Support creating subsets via napari Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

saeyslab/harpy#8 · Opened Mar 12, 2024
Work with scimap Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

saeyslab/harpy#4 · Opened Mar 12, 2024

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