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marcnol / pyHiM

Multiplexed DNA-FISH data analysis pipeline
GNU Lesser General Public License v3.0
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Deprecated "z-offset" for barcode-mask matching ? #241

Open XDevos opened 7 months ago

XDevos commented 7 months ago

During build_trace, when we transform the (x,y,z) localization of one spot to its pixel coordinates, here: https://github.com/marcnol/pyHiM/blob/e33e635d52d89a08f9e3a27218967bbc34428b4c/src/matrixOperations/build_traces.py#L161-L163

An offset is added for Z axes in commit 7b7b0ca to "compensate difference between barcode and DAPI channel":

https://github.com/marcnol/pyHiM/blob/7b7b0ca6d9b4e3532f9646e77caead29dfc210e8/src/fileProcessing/fileManagement.py#L296

And this value is 2 pixels by default. But now when we use primer or satellite masks, should we continue to use this offset ? Should we change the default value ?

XDevos commented 7 months ago

The parameter "z_offset" will be a dict like "masks2process":


{
    "...": "...",
    "masks2process": {"nuclei": "DAPI", "primer": "mask0"},
    "z_offset": {"nuclei": 2.0, "primer": 0.0},
    "...": "..."
}

We need to add a checker at the initialization of pyHiM.