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mahmoodlab
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HEST
HEST: Bringing Spatial Transcriptomics and Histopathology together
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add new samples and aligned transcripts
#53
pauldoucet
closed
5 days ago
0
What's the relation between coordinates in patches and coordinates in ST data?
#52
kennethahah
closed
5 days ago
6
One Xenium dataset on human breast cancer not in the database
#51
kennethahah
closed
2 weeks ago
3
Reproduce benchmark results
#50
judyueshen
closed
2 weeks ago
5
Refactor readthedocs
#49
pauldoucet
closed
2 weeks ago
0
Update 4-Running-HEST-Benchmark.ipynb
#48
guillaumejaume
closed
2 weeks ago
0
About patches in WSI
#47
Yoyiming
closed
2 weeks ago
8
Xenium datasets coordinates
#46
flyfyyfyy
opened
3 weeks ago
5
Image registration in Xenium dataset
#45
xiachenrui
closed
3 weeks ago
6
BCNB dataset
#44
hathawayxxh
closed
3 weeks ago
8
Do we need to correct the batch effects of given datasets
#43
HelloWorldLTY
opened
1 month ago
5
Update README.md
#42
guillaumejaume
closed
1 month ago
0
Add batch effect quantification methods
#41
pauldoucet
closed
1 month ago
0
negative value in adata.obsm['spatial']
#40
xiachenrui
closed
1 month ago
2
How large is the spot in Xenium data and ST data?
#39
kennethahah
closed
1 month ago
4
Matching cell type annotations with AnnData gene expression vectors
#38
merelkuijs
closed
1 day ago
11
add patch coordinates when saving to .h5
#37
pauldoucet
closed
1 month ago
0
256 x 256 patches for each spot instead of 224 x 224?
#36
kennethahah
closed
1 month ago
4
About cell type information
#35
nkuweili
closed
1 month ago
4
Pre-processed data for the multimodal representation learning task
#34
hathawayxxh
closed
1 month ago
5
cleanup bench + new foundation models
#33
pauldoucet
closed
1 month ago
0
rm unused imports
#32
guillaumejaume
closed
1 month ago
0
Import Error: ModuleNotFoundError for vision_transformer_latest
#31
oyjr
closed
1 month ago
4
move core methods to hestcore
#30
pauldoucet
closed
1 month ago
0
Wsi
#29
pauldoucet
closed
1 month ago
0
TENX98 and TENX97 don't have pixel/array coordinates
#28
KalinNonchev
closed
1 month ago
2
Why don't we use all the samples to construct the benchmark?
#27
huangtinglin
closed
1 month ago
2
fix exception thrown if cucim installed
#26
pauldoucet
closed
2 months ago
0
HEST-lib v1.1.0
#25
pauldoucet
closed
2 months ago
0
Update HEST_v1_0_0 -> HEST_v1_0_2
#24
pauldoucet
closed
2 months ago
0
add table with samples used in benchmark
#23
guillaumejaume
closed
2 months ago
0
The inclusion relationship between HEST and HEST Benchmark.
#22
Hanminghao
closed
2 months ago
1
Converting Hest data to Spatialdata
#21
SathiyaNManivannan
closed
2 months ago
1
Update README.md
#20
guillaumejaume
closed
2 months ago
0
add pip install datasets instruction
#19
pauldoucet
closed
2 months ago
0
setup autoapprove for HF repository
#18
pauldoucet
closed
2 months ago
0
Fix huggingface download counter
#17
pauldoucet
closed
2 months ago
0
high variance genes
#16
jinxixiang
opened
2 months ago
2
Normalize adata (found only log1p)
#15
rushin682
closed
2 months ago
3
fix bench gene panel
#14
pauldoucet
closed
3 months ago
0
low Pearson correlation for COAD, READ, HCC
#13
NBitBuilder
opened
3 months ago
8
Issue downloading datasets
#12
BioinfoTongLI
closed
3 months ago
2
Improve load_hest
#11
pauldoucet
closed
3 months ago
0
Update README.md
#10
pauldoucet
closed
3 months ago
0
add total size of dataset
#9
pauldoucet
closed
3 months ago
0
add adata description tutorial
#8
pauldoucet
closed
3 months ago
0
clear output
#7
guillaumejaume
closed
3 months ago
0
License
#6
guillaumejaume
closed
3 months ago
0
Update README.md
#5
guillaumejaume
closed
3 months ago
0
Add tutorials, make dataset public, resolve bugs
#4
pauldoucet
closed
3 months ago
0
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