Spatial data in cell browser #259
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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
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Hi, |
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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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Hi, 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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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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It is indeed 10x data. This is the original publication I think for your reference: https://pubmed.ncbi.nlm.nih.gov/35700707/. 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. |
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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.
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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.
>
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> Reply to this email directly, view it on GitHub
> <#259 (comment)>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AACL4TPBUAC6MANS7KSEZA3WQ6TBDANCNFSM6AAAAAATAROXI4>
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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... |
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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
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