mahmoodlab/HEST

Issues

• spot_diameter and spot_size_um in Xenium data

  #79 opened 20 days ago by Mengflz
  4

• Alignment spatial_plots for heart visium samples

  #78 opened a month ago by loicchadoutaud
  1

• Extra dependencies

  #76 opened a month ago by edoumazane
  2

• Aligning new HE-Xenium data

  #74 opened a month ago by alesroger
  3

• HEST installation on Windows fails with missing wheel error

  #72 opened 2 months ago by adiv5
  2

• Mapping gene names to Ensembl IDs

  #70 opened 2 months ago by JosephDiPalma
  3

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

  #62 opened 2 months ago by hugo-ekinge
  4

• Inconsistent samples between HEST-1k and HEST-bench

  #68 opened 2 months ago by huangtinglin
  4

• Xenium transcripts single-cell data analysis

  #67 opened 2 months ago by Arkkienkeli
  2

• Updated figure flipped species counts

  #64 opened 2 months ago by JosephDiPalma
  1

• The function save_spatial_plot does not align the HE image with spots on NCBI784

  #59 opened 2 months ago by kennethahah
  4

• How to use Xenium data for cell segmentations?

  #61 opened 2 months ago by schoonhovenrichard
  4

• Xenium datasets coordinates

  #46 opened 2 months ago by flyfyyfyy
  5

• Patches not normalized by pixel size

  #57 opened 2 months ago by yijiangchen
  6

• Regarding the Number of Patches and Spots in Xenium Dataset

  #60 opened 2 months ago by Yoyiming
  2

• Missing Data in Xenium "transcripts/" Folder?

  #56 opened 3 months ago by sky-lzy
  3

• About patches in WSI

  #47 opened 4 months ago by Yoyiming
  9

• Questions about image cropping

  #55 opened 3 months ago by HelloWorldLTY
  2

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

  #43 opened 4 months ago by HelloWorldLTY
  14

• Number of cells in human xenium samples

  #54 opened 3 months ago by kotr98
  3

• Matching cell type annotations with AnnData gene expression vectors

  #38 opened 3 months ago by merelkuijs
  11

• What's the relation between coordinates in patches and coordinates in ST data?

  #52 opened 3 months ago by kennethahah
  6

• One Xenium dataset on human breast cancer not in the database

  #51 opened 4 months ago by kennethahah
  3

• Reproduce benchmark results

  #50 opened 4 months ago by judyueshen
  5

• BCNB dataset

  #44 opened 4 months ago by hathawayxxh
  8

• Image registration in Xenium dataset

  #45 opened 4 months ago by xiachenrui
  6

• Pre-processed data for the multimodal representation learning task

  #34 opened 4 months ago by hathawayxxh
  5

• negative value in adata.obsm['spatial']

  #40 opened 4 months ago by xiachenrui
  2

• How large is the spot in Xenium data and ST data?

  #39 opened 4 months ago by kennethahah
  4

• 256 x 256 patches for each spot instead of 224 x 224?

  #36 opened 4 months ago by kennethahah
  4

• About cell type information

  #35 opened 5 months ago by nkuweili
  4

• Import Error: ModuleNotFoundError for vision_transformer_latest

  #31 opened 5 months ago by oyjr
  4

• TENX98 and TENX97 don't have pixel/array coordinates

  #28 opened 5 months ago by KalinNonchev
  2

• Why don't we use all the samples to construct the benchmark?

  #27 opened 5 months ago by huangtinglin
  2

• The inclusion relationship between HEST and HEST Benchmark.

  #22 opened 5 months ago by Hanminghao
  1

• Converting Hest data to Spatialdata

  #21 opened 5 months ago by SathiyaNManivannan
  1

• high variance genes

  #16 opened 6 months ago by jinxixiang
  2

• Normalize adata (found only log1p)

  #15 opened 6 months ago by rushin682
  3

• low Pearson correlation for COAD, READ, HCC

  #13 opened 6 months ago by NBitBuilder
  8

• Issue downloading datasets

  #12 opened 6 months ago by BioinfoTongLI
  2