Steps to use APIs

[justinesjw]

Hi,

Thank you for building this tool! I'm very excited to implement it.

I might have missed this but may I know where can I find the tutorial on steps to use the APIs? Do I sequentially implement these functions?

I've tried cross comparing the steps in CLI but failed to match the function names. Would really appreciate your help on this!

Thank you, Justine

[quentinblampey]

Hello @justinesjw,

Thanks for your interest in Sopa :)

For now, I only provide a documentation of the API. I will add in the next few weeks some tutorials on how to use the sopa.stats functions for instance, but I'm not sure to provide a tutorial for every API function because I thought most users may prefer using the CLI (or directly the Snakemake pipeline).

A few questions to understand what you want to do (this will help me to really answer your question and improve the documentation):

• Why do you prefer using the API rather than the CLI or Snakemake pipeline?
• What kind of segmentation to you want to perform (Cellpose? Baysor? Custom segmentation?)
• In which steps of Sopa (if not all) are you interest in? According to the illustration of the pipeline here: https://gustaveroussy.github.io/sopa/
• Are you familiar with the spatialdata library?

Thanks

[justinesjw]

Hello @quentinblampey,

Thanks for your reply. :) Awesome! Excited for your tutorials. Will try out Snakemake pipeline!

Regarding the questions: Q1 : As I am more familiar with R and Python, I would prefer API over CLI/snakemake. Also, for documentation purposes, I'm interested in a library which can streamline my scripts. Currently, I am running Baysor on it's own.

Q2/3 : I am interested in cell segmentation and do not have any preference on methods. Similar to most, I noticed that the default Xenium segmentation mis-segment a high portion of cells and would like to see how other methods perform? I am also excited to use your explorer function!

Q4 : My analyses are heavier on R packages though I am starting to use Squidpy which helped me understand spatialdata structures.

Thanks!

Best, Justine

[quentinblampey]

Hello @justinesjw,

Thanks for your answers, I better understand your usage now! Indeed, if you want to include Sopa into your own scripts, then the API is the best way to go. I just wanted to make sure that this was what you wanted (because the snakemake pipeline or the CLI are usually the first choices).

I finally released version 1.0.2 with the new tutorial on the API usage. I will be happy to improve this tutorial based on your feedback!

NB: some commands of this tutorial are specific to sopa 1.0.2, so make sure to get the latest version

[quentinblampey]

Hello @justinesjw, have you had a chance to look at the tutorials? If you have some questions, I'll be happy to help, and I can update the API tutorial. Else, if everything is clear, let me know if I can close the issue!

[justinesjw]

Hey @quentinblampey,

Thanks for the tutorials, they were helpful and informative! I'm still exploring among platforms!

I'll close this issue for now.

[quentinblampey]

Ok great! Don't hesitate to re-open it in the future if you have new questions 🙂