search

QIFEIDKN / STAGATE

Adaptive Graph Attention Auto-encoder for Spatial Domain Identification of Spatial Transcriptomics
MIT License
36 stars 19 forks source link

About datasets used in your paper: How to get Layer structure labels of STARmap dataset? #11

Open BinDuan opened 2 years ago

BinDuan commented 2 years ago

Congratulations for this nice work! I am very interested in the performace for STARmap datasets and I wonder how do you get the layer structure label of STARmap dataset, because I can't find it in the website you provide. I'll appreciate it if you can explain this or provide the layer structure label.

Thanks!

xiao-kong-long commented 2 years ago

Hello, I have similar problem with you, I can't find the 'tissue_positions_list.csv' in tutorial 2, I don't know whether you find it

xiao-kong-long commented 2 years ago

Hello, I have similar problem with you, I can't find the 'tissue_positions_list.csv' in tutorial 2, I don't know whether you find it

I find it in there image

BinDuan commented 2 years ago

Hello, I have similar problem with you, I can't find the 'tissue_positions_list.csv' in tutorial 2, I don't know whether you find it

I find it in there image

Thank you for your sharing, can you share the website?

xiao-kong-long commented 2 years ago

Hello, I have similar problem with you, I can't find the 'tissue_positions_list.csv' in tutorial 2, I don't know whether you find it

I find it in there image

Thank you for your sharing, can you share the website?

hello, it's dataset in tutorial 2, maybe not useful to you

QIFEIDKN commented 2 years ago

We add a Tutorial of the ISH-based STARmap dataset (i.e. the Fig. S16 of the STAGATE paper) at https://stagate.readthedocs.io/en/latest/T9_STARmap.html. The layer annotation of the STARmap data are provided by the SpaGCN paper, and you can found it at the adata.obs['labels'] in our tutorial.

BinDuan commented 2 years ago

We add a Tutorial of the ISH-based STARmap dataset (i.e. the Fig. S16 of the STAGATE paper) at https://stagate.readthedocs.io/en/latest/T9_STARmap.html. The layer annotation of the STARmap data are provided by the SpaGCN paper, and you can found it at the adata.obs['labels'] in our tutorial.

Thank you so much!