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maximilianh / cellBrowser

main repo: https://github.com/ucscGenomeBrowser/cellBrowser/ - Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org
https://github.com/ucscGenomeBrowser/cellBrowser/
GNU General Public License v3.0
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Spatial data in cell browser #259

Open cancerGen opened 1 year ago

cancerGen commented 1 year ago

Hi I was wondering if there is any way to use/explore spatial data in cell browser? Something similar to Loupe browser if possible

Thanks

maximilianh commented 1 year ago

Yes I’m just committing it! I have 15 spatial datasets up, but hidden because they’re not my datasets.

Is your file 10X visium or something else ? Could you share it so I can test it ? Can I follow up by direct email in case it’s not published yet ?

On Thu 15 Dec 2022 at 22:26, cancerGen @.***> wrote:

Hi I was wondering if there is any way to use/explore spatial data in cell browser? Something similar to Loupe browser if possible

Thanks

— Reply to this email directly, view it on GitHub https://github.com/maximilianh/cellBrowser/issues/259, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TML6UPZ3XVVC6QTOF3WNQDSDANCNFSM6AAAAAATAROXI4 . You are receiving this because you are subscribed to this thread.Message ID: @.***>

cancerGen commented 1 year ago

Hi, I am actually using public data and have not generated any data myself. Can I check out the browser?

maximilianh commented 1 year ago

Can you point me to some spatial public dataset such that I can use it to show you the feature? The only two datasets I have now are pre-publication and their authors do not want me to share the links. But the importers handle 10X just fine, so hopefully adding a spatial dataset won't be too much work. Thanks for your patience with this, the holidays delayed the response.

On Mon, Dec 19, 2022 at 7:19 AM cancerGen @.***> wrote:

Hi, I am actually using public data and have not generated any data myself. Can I check out the browser?

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cancerGen commented 1 year ago

Hi, So I am using this data from the SPATA paper. The data download tutorial is provided here: https://github.com/theMILOlab/SPATAData

If you could load any one of these samples for me to explore the browser it will be very helpful. Thanks

maximilianh commented 1 year ago

Uhhh.... I see. But I've never seen this data format... Do you know if the SPATA project has normal 10X Visium .h5 files somewhere? Is this actually Visium data?

On Thu, Jan 5, 2023 at 4:47 PM cancerGen @.***> wrote:

Hi, So I am using this data from the SPATA paper. The data download tutorial is provided here: https://github.com/theMILOlab/SPATAData

If you could load any one of these samples for me to explore the browser it will be very helpful. Thanks

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cancerGen commented 1 year ago

It is indeed 10x data. This is the original publication I think for your reference: https://pubmed.ncbi.nlm.nih.gov/35700707/. You can download the SPATA2 objects using R and convert it into Seurat object using the following function. https://rdrr.io/github/kueckelj/SPATA2/man/transformSpataToSeurat.html

Could you please tell me what is supposed to be the input format for the UCSC spatial data browser? I could write a small script to help you get the files in a correct format.

maximilianh commented 1 year ago

I dropped the ball on this sorry. The spatial part right now can read either h5AD scanpy images or just normal jpeg or PNG files with the min/max range specified of the overlaid coordinates. It will scale the coordinates.

So just providing the image in the cellbrowser.conf file should work in most cases. We still have not released the code, but you can always use the "develop" branch..

On Fri, Jan 6, 2023 at 6:16 AM cancerGen @.***> wrote:

It is indeed 10x data. This is the original publication I think for your reference: https://pubmed.ncbi.nlm.nih.gov/35700707/. You can download the SPATA2 objects using R and convert it into Seurat object using the following function. https://rdrr.io/github/kueckelj/SPATA2/man/transformSpataToSeurat.html

Could you please tell me what is supposed to be the input format for the UCSC spatial data browser? I could write a small script to help you get the files in a correct format.

— Reply to this email directly, view it on GitHub https://github.com/maximilianh/cellBrowser/issues/259#issuecomment-1373156494, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TPBUAC6MANS7KSEZA3WQ6TBDANCNFSM6AAAAAATAROXI4 . You are receiving this because you commented.Message ID: @.***>

maximilianh commented 1 year ago

Alternatively, you can just send us a Seurat or Scanpy object and the spatial image behind it in any image format.

On Tue, Feb 7, 2023 at 2:54 PM Maximilian Haeussler @.***> wrote:

I dropped the ball on this sorry. The spatial part right now can read either h5AD scanpy images or just normal jpeg or PNG files with the min/max range specified of the overlaid coordinates. It will scale the coordinates.

So just providing the image in the cellbrowser.conf file should work in most cases. We still have not released the code, but you can always use the "develop" branch..

On Fri, Jan 6, 2023 at 6:16 AM cancerGen @.***> wrote:

It is indeed 10x data. This is the original publication I think for your reference: https://pubmed.ncbi.nlm.nih.gov/35700707/. You can download the SPATA2 objects using R and convert it into Seurat object using the following function. https://rdrr.io/github/kueckelj/SPATA2/man/transformSpataToSeurat.html

Could you please tell me what is supposed to be the input format for the UCSC spatial data browser? I could write a small script to help you get the files in a correct format.

— Reply to this email directly, view it on GitHub https://github.com/maximilianh/cellBrowser/issues/259#issuecomment-1373156494, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TPBUAC6MANS7KSEZA3WQ6TBDANCNFSM6AAAAAATAROXI4 . You are receiving this because you commented.Message ID: @.***>

maximilianh commented 1 year ago

Oh by the way that code is committed now and the example cellbrowser configuration should have an example.

What i don't have yet is a sample dataset... maybe I should use a pbmc3k-spatial or some similar common demo dataset...