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leeju-umich / Cho_Xi_Seqscope

Seqscope codes
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Alignment between H&E histology image and Seq-scope spatial transcriptome data #2

Closed DongqingSun96 closed 2 years ago

DongqingSun96 commented 3 years ago

Hi, thanks for providing these scripts to show how to process Seq-scope. I have a question about the alignment between H&E histology image and Seq-scope spatial transcriptome data. How can we know the matched HDMI coordinates for one pixel in the H&E histology image? I would appreciate it if you could give me some help. Thanks!

leeju-umich commented 3 years ago

Dear Dongqing,

Thank you for the question. Since we did not implement a fiducial marker here, we used all the information we have (cell type, tissue boundary, etc.) to get the best image-transcriptome alignment possible. The process was completely manual. I hope this helps.

All the best, Jun Hee

On Thu, Sep 16, 2021 at 2:09 AM Dongqing Sun @.***> wrote:

Hi, thanks for providing these scripts to show how to process Seq-scope. I have a question about the alignment between H&E histology image and Seq-scope spatial transcriptome data. How can we know the matched HDMI coordinates for one pixel in the H&E histology image? I would appreciate it if you could give me some help. Thanks!

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Jun Hee Lee, Ph.D. Associate Professor Department of Molecular and Integrative Physiology University of Michigan Geriatrics Center 109 Zina Pitcher Place, 3019 BSRB Ann Arbor, MI 48109-2200 Office: 734-764-6789 | Lab: 734-764-6795 Fax: 734-936-9220 | E-mail: @.*** https://lee.lab.medicine.umich.edu/

DongqingSun96 commented 3 years ago

Dear Dr. Lee,

Thanks for your reply. If it is convenient, could you please provide the image-transcriptome alignment result that you used in the paper? Thank you so much!

Best, Dongqing

leeju-umich commented 3 years ago

You would be able to find it in Fig S4J in our paper. The single cell transcriptome data and histology pictures are available at https://doi.org/10.7302/cjfe-wa35

Best, Jun Hee

On Sat, Sep 18, 2021 at 8:26 AM Dongqing Sun @.***> wrote:

Dear Dr. Lee,

Thanks for your reply. If it is convenient, could you please provide the image-transcriptome alignment result that you used in the paper? Thank you so much!

Best, Dongqing

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/leeju-umich/Cho_Xi_Seqscope/issues/2#issuecomment-922269182, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQLZFMLLLUZEAFSDBZXVSNDUCSAOZANCNFSM5ED7EGFA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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Jun Hee Lee, Ph.D. Associate Professor Department of Molecular and Integrative Physiology University of Michigan Geriatrics Center 109 Zina Pitcher Place, 3019 BSRB Ann Arbor, MI 48109-2200 Office: 734-764-6789 | Lab: 734-764-6795 Fax: 734-936-9220 | E-mail: @.*** https://lee.lab.medicine.umich.edu/