Downstream analysis?

[Agrajag1984]

Hi I used the old mesmerize and found all the downstream analysis possibilities rather helpful. I cant, however, figure out, whether the new mesmerize-core offers equal tools and if so, how to use them.
Kind regards and thank you in advance

[kushalkolar]

Hi, we do not provide downstream analysis and from our experience providing a GUI in the form of a flowchart for downstream analysis in the olde mesmerize mostly led users to creating things that looked like they made sense without really understanding the underlying analysis. And the barrier for users was on the side of understanding downstream analysis rather than basic programming.

I recommend using pynapple and the rest of the scientific python ecosystem (sklearn, tslearn, etc.) for any downstream analysis.

[Agrajag1984]

To be honest I dont understand the output of mesmerize Core. I am looking to extract basic ephys parameters like peak, rise time half width etc. in mesmerize there was a table after selecting peaks. Is this stll possible or do I need to code a peak extraction software to extract the parameters from a trace-like file?
Kind regards

[kushalkolar]

All the outputs can be accessed for example like this: df.iloc[index].cnmf.get_temporal .

Are you analyzing non-spiking cells (ex. development?)

[Agrajag1984]

Thank you very much! Unfortunately I still dont understand the structure of the resulting df. Using your example code from the cnmfe notebook the command you mentioned results in shape (365, 3000), what is columns? what is rows? is there a way to get the spatial data? where and how is it saved?

[kushalkolar]

This is all explained in the user guide and CNMF API docs