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LieberInstitute / VistoSeg

Image processing pipeline for spatial projects
http://research.libd.org/VistoSeg/
GNU General Public License v3.0
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Explain how to download the data used in this documentation #2

Closed lcolladotor closed 3 years ago

lcolladotor commented 3 years ago

Similar to #1, at https://github.com/LieberInstitute/VisiumImgProcessing/blob/705329a25b21f818e62a3606fec4a7af1f757192/Step1.Rmd#L3 or maybe before, I would add a code chunk or description telling readers where they can download these images from. You might want to use the AWS links we have at https://github.com/LieberInstitute/spatialLIBD#raw-data. If you do, make sure the file names match the ones you use in your commands.

Basically, we want readers to be able to run the commands described here on their own computers. This is useful to detect if there are any issues related to software versions or operating systems. That is, users shouldn't get any errors from running these commands, but if they do, we'd want them to report the problem(s) and fix the issues. So in essence, we are giving them a small reproducible example and describing it in this documentation.

lcolladotor commented 3 years ago

Based on #5, if the data you are using for the examples is relatively small, we could include it in this repository. Similar to http://research.libd.org/SPEAQeasy-example/prepare_data.html.

Though hm... I see that the image you are showing on #5 is 26 GB and it's unpublished. Hm...

$ ls  -lh /dcl02/lieber/ajaffe/SpatialTranscriptomics/LIBD/spatialDLPFC/Images/Liebert_Institute_OTS-20-7748_rush_posterior.tif
-rwxrwx--- 1 mtippani lieber_jaffe 26G Nov 19 17:00 /dcl02/lieber/ajaffe/SpatialTranscriptomics/LIBD/spatialDLPFC/Images/Liebert_Institute_OTS-20-7748_rush_posterior.tif

So, it might make sense to use a smaller example if possible. Though here it depends if that exists. Like, can we use any data from https://support.10xgenomics.com/spatial-gene-expression/datasets for this documentation? Or does it only really apply to our new spatialDLPFC data?

lcolladotor commented 3 years ago

If we really need to, we can think about making /dcl02/lieber/ajaffe/SpatialTranscriptomics/LIBD/spatialDLPFC/Images/Liebert_Institute_OTS-20-7748_rush_posterior.tif public though (likely through AWS).