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reillytilbury / coppafish

Python version of iss software
MIT License
4 stars 2 forks source link

Add new call spots #283

Closed reillytilbury closed 3 months ago

reillytilbury commented 4 months ago

Add new call spots with updated page variable names, new methods and new diagnostics.

reillytilbury commented 4 months ago

This involves a large reorganisation of some variables. Given that we are trying to make this a stable version so we don't have to rerun data, let's try get as many notebook name changes out of the way as soon as possible.

So @paulshuker this is probably a good time to remove the background and use_preseq options from notebook pages.

I will also remove the absolute intensity percentile from call spots, as it makes more sense to compute this in OMP given that we load the entire tile in at that point. This also raises the point that we can compute a different intensity threshold for each tile which might be worthwhile!