Input structure to run Akoya CODEX data

[Lucas-Maciel]

Hi,

I'm very interested in using MCMICRO in my own data, however, I'm a bit confused about how to structure my own data. I have Akoya CODEX data and each sample has several subfolders corresponding to the different tiles.

I have read the documentation about the input (https://mcmicro.org/io.html#input) but it's not clear to me how should I set the markers.csv file in order to recognize the suffix in the images and if I need to provide something in the parameters related to the coordinates of the tiles.

Thanks for your help

[jmuhlich]

Could you answer a couple of questions?

• Which specific instrument was used here? There are a few different generations of CODEX.
• Do you have multiple Z-planes in these images or are they all z001?

[Lucas-Maciel]

Hi @jmuhlich

We used the phenocycler(codex) coupled to a keyence BZ-X810
No, there is only one Z-plane

Thanks

[sminot]

I have a similar set of input data from analogous instrumentation, and would really appreciate any guidance you have on how mcmicro could be used to process this data. In my case, there are multiple Z-planes which need to be deconvolved to find the best focal plane, if possible.

Many thanks for any help you can provide.