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Very elegant work, but I think you omitted a key procedure about how to translate a raw data file of MALDI (usually as imzML format)into h5ad object, which can be recognized by scanpy. Could you compl…
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It's turning out to be quite difficult to get MALDI data into a format that works with MSQL.
Note: I don't currently have access to any Vendor software to see what it can export.
My first go-to…
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Hello, when I try to run the example (e.g. warp_tof_spheroids.py), the IDE says,
> FileNotFoundError: [Errno 2] No such file or directory: 'datasets/tof-spheroids/spheroids-no_normalization.sbd'.
…
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## Background
Raw forms of MSI data in imzML are perfectly appropriate and should be served. But preprocessed forms can also be useful. There may be a large knowledge gap for someone coming from, let…
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Hi, I'm a developer on the [METASPACE](https://metaspace2020.eu) project.
I'm investigating methods for imzML file recalibration in conjunction with molecular databases (HMDB, lists of theoretical…
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I am trying to convert some HeLa sample generated raw data and on an average it takes about couple of hours, for example
```
timsconvert --chunk_size 10000000 --imzml_mode continuous --verbose --i…
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It would be nice if there was the option to generate a scale bar for ion images. Ideally read from the imzml but even a manual input one would be great.
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add group name, so that files are called "name"_"group".imzml
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Dear Karsten Wüllems,
I’m a Ph.D student in France on Brassica napus (rapeseed) specialized metabolites against pathogens. I want to apply your pipeline “Analysis of GRaph mapped Image data NEtwor…
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I am trying to finish a pipeline that takes data collected on a combined Thermo Velos, Spectroglyph source, and Predator data station based acquisition into imzML. I am currently at the point where I …