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mahmoodlab
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HEST
HEST: Bringing Spatial Transcriptomics and Histopathology together - NeurIPS 2024
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add doc for XeniumReader and ensemblID to gene names
#75
pauldoucet
closed
4 hours ago
0
Aligning new HE-Xenium data
#74
alesroger
opened
1 day ago
1
Make HEST-Benchmark deterministic
#73
guillaumejaume
closed
1 week ago
0
HEST installation on Windows fails with missing wheel error
#72
adiv5
closed
1 week ago
2
HESTData: provide util to map ensemble ID to gene name
#71
konst-int-i
closed
1 week ago
3
Mapping gene names to Ensembl IDs
#70
JosephDiPalma
opened
2 weeks ago
3
add dask suppport and valis alignment
#69
pauldoucet
closed
2 weeks ago
0
Inconsistent samples between HEST-1k and HEST-bench
#68
huangtinglin
closed
2 weeks ago
4
Xenium transcripts single-cell data analysis
#67
Arkkienkeli
closed
2 weeks ago
2
Update README.md
#66
guillaumejaume
closed
2 weeks ago
0
Guillaumejaume patch 1
#65
guillaumejaume
closed
2 weeks ago
0
Updated figure flipped species counts
#64
JosephDiPalma
closed
2 weeks ago
1
HESTData: update `to_spatial_data()```
#63
konst-int-i
closed
3 weeks ago
3
Barcodes loaded in inconsistent format (different data types based on batch size)
#62
hugo-ekinge
opened
3 weeks ago
4
How to use Xenium data for cell segmentations?
#61
schoonhovenrichard
closed
3 weeks ago
4
Regarding the Number of Patches and Spots in Xenium Dataset
#60
Yoyiming
closed
4 weeks ago
2
The function save_spatial_plot does not align the HE image with spots on NCBI784
#59
kennethahah
closed
3 weeks ago
4
Update README.md
#58
guillaumejaume
closed
3 weeks ago
0
Patches not normalized by pixel size
#57
yijiangchen
closed
3 weeks ago
6
Missing Data in Xenium "transcripts/" Folder?
#56
sky-lzy
closed
1 month ago
3
Questions about image cropping
#55
HelloWorldLTY
closed
1 month ago
2
Number of cells in human xenium samples
#54
kotr98
closed
1 month ago
3
add new samples and aligned transcripts
#53
pauldoucet
closed
1 month ago
0
What's the relation between coordinates in patches and coordinates in ST data?
#52
kennethahah
closed
1 month ago
6
One Xenium dataset on human breast cancer not in the database
#51
kennethahah
closed
2 months ago
3
Reproduce benchmark results
#50
judyueshen
closed
2 months ago
5
Refactor readthedocs
#49
pauldoucet
closed
2 months ago
0
Update 4-Running-HEST-Benchmark.ipynb
#48
guillaumejaume
closed
2 months ago
0
About patches in WSI
#47
Yoyiming
closed
2 months ago
9
Xenium datasets coordinates
#46
flyfyyfyy
closed
3 weeks ago
5
Image registration in Xenium dataset
#45
xiachenrui
closed
2 months ago
6
BCNB dataset
#44
hathawayxxh
closed
2 months ago
8
Do we need to correct the batch effects of given datasets
#43
HelloWorldLTY
opened
2 months ago
14
Update README.md
#42
guillaumejaume
closed
2 months ago
0
Add batch effect quantification methods
#41
pauldoucet
closed
2 months ago
0
negative value in adata.obsm['spatial']
#40
xiachenrui
closed
2 months ago
2
How large is the spot in Xenium data and ST data?
#39
kennethahah
closed
3 months ago
4
Matching cell type annotations with AnnData gene expression vectors
#38
merelkuijs
closed
1 month ago
11
add patch coordinates when saving to .h5
#37
pauldoucet
closed
3 months ago
0
256 x 256 patches for each spot instead of 224 x 224?
#36
kennethahah
closed
3 months ago
4
About cell type information
#35
nkuweili
closed
3 months ago
4
Pre-processed data for the multimodal representation learning task
#34
hathawayxxh
closed
2 months ago
5
cleanup bench + new foundation models
#33
pauldoucet
closed
3 months ago
0
rm unused imports
#32
guillaumejaume
closed
3 months ago
0
Import Error: ModuleNotFoundError for vision_transformer_latest
#31
oyjr
closed
3 months ago
4
move core methods to hestcore
#30
pauldoucet
closed
3 months ago
0
Wsi
#29
pauldoucet
closed
3 months ago
0
TENX98 and TENX97 don't have pixel/array coordinates
#28
KalinNonchev
closed
3 months ago
2
Why don't we use all the samples to construct the benchmark?
#27
huangtinglin
closed
3 months ago
2
fix exception thrown if cucim installed
#26
pauldoucet
closed
3 months ago
0
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