Issues

• HEST-Benchmark: README and paper Table A13 specify different probing protocols, and they rank models differently

  mahmoodlab/HEST#144 · Filter by author stalinnn opened on Sep 3, 2026

• "pool_bins_visiumhd" loses most UMIs (fancy-index += doesn't accumulate)

  mahmoodlab/HEST#143 · Filter by author Kyyle2114 opened on Aug 10, 2026

• Question about separating FFPE and FF samples in Hestbench?

  mahmoodlab/HEST#142 · Filter by author alexaex opened on Jul 1, 2026

• Clarify HEST public benchmark protocol

  mahmoodlab/HEST#141 · Filter by author yubin-ai opened on May 21, 2026

• Correcting error in pool_transcripts_xenium when pandas object

  mahmoodlab/HEST#138 · Filter by author AndrejPer opened on Apr 25, 2026

• Error with valis-hest

  mahmoodlab/HEST#119 · Filter by author Kexin-xu-01 opened on Oct 13, 2025
  1

  

• Access to additional info. in xenium spatial data

  mahmoodlab/HEST#118 · Filter by author DabinJeong opened on Oct 2, 2025
  1

• Adding GrandQC Artefact Filtering

  mahmoodlab/HEST#117 · Filter by author Kexin-xu-01 opened on Sep 10, 2025
  1

• Incorporate Newer Foundation Models

  mahmoodlab/HEST#116 · Filter by author Kexin-xu-01 opened on Sep 8, 2025
  1

• "pip install" skips local_ckpts.json

  mahmoodlab/HEST#115 · Filter by author aowenson-imm opened on Sep 8, 2025

• Dependency conflict with new xarray packages

  mahmoodlab/HEST#113 · Filter by author rushin682 opened on Aug 12, 2025
  2

• Xenium cell_id in transcripts and CellVit segmentation results

  mahmoodlab/HEST#109 · Filter by author Szym29 opened on Jun 14, 2025
  2

• Adapting SpatialData to naming restrictions for HEST samples

  mahmoodlab/HEST#104 · Filter by author rushin682 opened on Apr 27, 2025
  4

• st.save() error: only length-1 arrays can be converted to Python scalars

  mahmoodlab/HEST#99 · Filter by author katimbach opened on Apr 17, 2025
  5

• Loading raw Xenium data

  mahmoodlab/HEST#97 · Filter by author ekansh09 opened on Apr 2, 2025
  1

• UnboundLocalError: local variable 'pyvips' referenced before assignment

  installation
  mahmoodlab/HEST#95 · Filter by author ShinHyun-soo opened on Feb 27, 2025
  1

  

• Is contrast enhancement applied on extracted patches ?

  mahmoodlab/HEST#93 · Filter by author abhi1998goyal opened on Feb 6, 2025
  5

• Error in downloading the EPM cancer Visium data

  mahmoodlab/HEST#91 · Filter by author aahsan045 opened on Feb 4, 2025
  2

• Patching of the BCNB dataset

  mahmoodlab/HEST#90 · Filter by author hathawayxxh opened on Feb 3, 2025
  1

• Multi-channel whole-slide image dataset.

  question
  mahmoodlab/HEST#84 · Filter by author Algolzw opened on Jan 2, 2025
  1

• Barcodes loaded in inconsistent format (different data types based on batch size)

  mahmoodlab/HEST#62 · Filter by author hugo-ekinge opened on Oct 29, 2024
  5

• Do we need to correct the batch effects of given datasets

  scientific-discussion
  mahmoodlab/HEST#43 · Filter by author HelloWorldLTY opened on Aug 30, 2024
  14

• high variance genes

  scientific-discussion
  mahmoodlab/HEST#16 · Filter by author jinxixiang opened on Jul 6, 2024
  2