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MS-imaging support / MsBackendImzML

Open RogerGinBer opened this issue 1 month ago • 2 comments

Hi there! In our research group we are actively working with MS-imaging (MSI) data and I was wondering about how to properly name and add the spatial coordinates information to a MsBackend object and whether we should also define generics for them in Spectra. Basically, for each MSI spectra, you have a pair of x and y coordinates, so it seems natural to add them as spectraData in two separate columns

For context, I recently created a new backend (WIP) for imzML/ibd files (https://github.com/RogerGinBer/MsBackendImzML), which parses imzML files and saves each scan information (similar to header in mzR) and offsets in a DFrame as SpectraData. The actual peaksData is retrieved on-demand from the ibd files.

Provisionally, I'm saving the x and y coordinates as xPixel and yPixel (because x and y were too generic IMO), but since this information may also appear in other backends that can/could handle MS-imaging data (thinking of MsBackendTimsTof, but also maybe MsBackendRawFileReader), I think I'd be nice if we could do some brainstorming about this

RogerGinBer avatar May 17 '24 08:05 RogerGinBer