add functions readXeniumSPE(), readCosmxSPE(), readMerscopeSPE(), and example data

[estellad]

Hi there,

I tried using MoleculeExperiment (ME) read in these new imaging technology data and coerce them to SPE, but the process is a bit long and bulky. Here these 3 functions directly read in the data as SPE at single-cell level (rather than ME at transcript level and then SPE at single-cell level). I also added example data to the /inst/extdata/* folders.

I have not updated the NAMESPACE to export them, so please review first and let me know.

Sincerely,
Estella

[drighelli]

Thanks Estella,

I think this could be of great help!

I just accepted to run the checks, I'll take a look to the code as soon as I can!

DArio

[estellad]

@lmweber Hi Lukas, would you like to review? -- Thanks, Estella :D

[lmweber]

Hi @estellad , thank you, yes I will have a look at this soon!

[lmweber]

Hi @estellad , thanks again for this PR. I'm following up to let you know we are currently in the middle of some discussions about whether to move all the reader functions (including the existing one read10xVisium()) into a separate package, so that we can streamline the dependencies and longer-term maintenance required for SpatialExperiment.

We (@drighelli @HelenaLC ) will be discussing this and where it is up to some more in a meeting next week, so for now I think it will be better if we wait until after this meeting to finish reviewing this PR. Once we have an agreed plan, we will let you know about where (i.e. which package) we can add these functions and any updates. Does this sound ok to you?

[estellad]

Hi @lmweber ,

Thank you for initiating the discussion! Sorry for the late reply as I was on vacation.
I agree with you on moving these to a new package. I will continue the discussion in #126

Sincerely,
Estella

[lmweber]

Hi all, updating this discussion to mention that @estellad has now submitted the separate reader package SpatialExperimentIO to Bioc: Bioconductor/Contributions#3342. This contains functions for CosMx, MERSCOPE, Xenium, and STARmap. The function for Visium will remain in the SpatialExperiment package for now, and we can discuss again later if we want to move it. Thank you @estellad !

I'll leave this PR / discussion open for now so that we can easily refer to it if we need to while SpatialExperimentIO goes through the Bioc reviews, and then will plan to close this PR later (depending on whether SpatialExperimentIO goes into this Bioc cycle or the next one).

[lmweber]

Also leaving a link to the VisiumIO package here (which is in Bioc-devel now) so we have all the links in one place: https://github.com/waldronlab/VisiumIO

[drighelli]

Thanks Lukas @lmweber and Estella @estellad,

I also looked into the Estella's functions in the past, used and made some changes by myself, once I have a final version I'll make a PR on hers github repo.

Nice work!

[estellad]

Hi @drighelli Thank you for your upcoming pull request!
I am making some final updates before submitting them to Bioc before the deadline tomorrow. I will let you know when I finish my updates by today.