Is it possible to provide a mannual annotation file for HCC dataset?

feiyoung / PRECAST

an efficient data integration method for multiple spatial transcriptomics data with non- cluster-relevant eﬀects such as the complex batch eﬀects.

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Is it possible to provide a mannual annotation file for HCC dataset? #21

Open JunjieXia14 opened 3 months ago

JunjieXia14 commented 3 months ago

Hi,

This is excellent work. I am interested in utilizing the HCC dataset for further analysis. Could you provide detailed manual annotations for each spot?

Thanks for your kind help.

Best

feiyoung commented 3 months ago

The raw data in the PRECAST paper only includes annotations that are directly applied to the H&E images by pathologist, as demonstrated in the bottom panel of Figure 5a. You can access the manually annotated data, based on the clusters derived from PRECAST, at the following GitHub repository link: https://github.com/feiyoung/PRECAST_Analysis/tree/main/Real_data_analysis/data/meta.data_HCCx.csv. Here, you will find the 'precast.clusters' and 'manual.annotation' columns, which provide the cluster assignments and corresponding manual annotations, respectively.

JunjieXia14 commented 3 months ago

Hi feiyoung,

Thank you for your quick and kind reply. I am very interested in the raw spot annotations from the H&E images by the pathologist. Could you please share this file with me?

Thanks again.

feiyoung commented 3 months ago

The raw data in the PRECAST paper only includes annotations that are directly applied to the H&E images by pathologist,

I may not have expressed myself clearly. We do not possess the file containing raw spot annotations, but only the annotated H&E images.