How to run NCEM for CODEX csv/or FCS output data?

[DRSEI]

Question

Hi I want to use NCEM for CODEX data , but I could find any tutorial or how to prepare the data for this type of analysis.

Could please direct me if there is any tutorial or notebook that you could share with us ?

[AnnaChristina]

Thanks for raising the questions. I assume your data is stored in a csv file?

Ncem for custom data depends on AnnData as an input data object. More information on how to store your data as an AnnData ibject can be found in the following three documentations:

• AnnData documentation: https://anndata.readthedocs.io/en/latest/
• Scanpy documentation: https://scanpy.readthedocs.io/en/stable/
• Squidpy documentation: https://squidpy.readthedocs.io/en/stable/#

I hope this helps and please reach out again in case of further questions

[DRSEI]

Hello @AnnaChristina Thank you for taking the time to respond to my comments. I am using CODEX output and have segmented it using Qpath. The file includes x and y coordinates with gene/protein expression matrices for annotated markers in CSV format. I was wondering if you could provide me with more information about your analysis of the CODEX dataset. Specifically, I am curious about what type of output you used from CODEX itself or from other software. Additionally, I would like to know which segmentation pipeline you used.

The reason for my inquiry is that I want to ensure that I am following the correct pipeline to generate my results. Any information or guidance you could provide on this matter would be greatly appreciated.

Thank you for your help.