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maaskola / spatial-transcriptome-deconvolution

Index of repositories for code to perform spatial transcriptome deconvolution.
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How to map spots to HE #1

Open cquzys opened 2 years ago

cquzys commented 2 years ago

Hi author: I downloaded the ST datasets from the paper 'Berglund, E. et al. Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity. Nat. Commun. 9, 2419 (2018).'. However, the dataset only provides rows and columns while not pixel coordinates in Histology images. Thus, I couldn't map spot to Histology images！

Can you help me solve it?

Thanks!

Sudolin commented 2 years ago

Hi author: I downloaded the ST datasets from the paper 'Berglund, E. et al. Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity. Nat. Commun. 9, 2419 (2018).'. However, the dataset only provides rows and columns while not pixel coordinates in Histology images. Thus, I couldn't map spot to Histology images！

Can you help me solve it?

Thanks!

Hi! I failed to download this count matrix probably due to invalid link provided in the paper. Could you please tell me where and how I could get the count matirx? Thanks in advance.

cquzys commented 2 years ago

Links: 1) https://spatialtranscriptomics3d.shinyapps.io/STProstateResearch/ 2) https://www.spatialresearch.org/resources-published-datasets/10-1038-s41467-018-04724-5/

hah2468 commented 7 months ago

Hi author: I downloaded the ST datasets from the paper 'Berglund, E. et al. Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity. Nat. Commun. 9, 2419 (2018).'. However, the dataset only provides rows and columns while not pixel coordinates in Histology images. Thus, I couldn't map spot to Histology images！

Can you help me solve it?

Thanks!

Hi! I once found a similar example of annotation from HE in a GitHub repository, which might be helpful. https://github.com/BiomedicalMachineLearning/Spacell/blob/master/tutorial/Tutorial_Spacell_validation.ipynb

Additionally, where did you download the uncompressed HE images? I couldn't find the download link from the link you provided. If you have uncompressed HE images, I would be very grateful.