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AlanRace / jimzMLParser

Java imzML (mass spectrometry imaging) and mzML (mass spectrometry) parser
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Any way to make use this repo and open imzml files in ImageJ / Fiji ? #3

Closed NicoKiaru closed 9 months ago

NicoKiaru commented 9 months ago

Hello!

I recently had to deal with the imzml format, and since I couldn't easily open imzml files, users have been giving me uncalibrated png images with an extra frame and where pixels are not mapped 1 to 1 to spectrum but interpolated. That's becoming annoying and I'd like to improve the situation for ImageJ /Fiji. I've seen a few python-based repos that could open imzml dataset, but nothing in Java so far until I saw your repo!

I want to see if there's a way to use it for ImageJ / Fiji. Do you think it's possible ? How much effort do you anticipate it would require? What I have in mind is either to build on your repo to make an ImagePlus object, or ideally a bio-formats reader. Since the data are generally big, it would be nice to have a lazy access to data.

I'm struggling a bit to understand the file format. The book chapter (https://link.springer.com/protocol/10.1007/978-1-60761-987-1_12) is not open-access, and there's a number of broken links I found:

In the page https://ms-imaging.org/imzml/controlled-vocabulary/:

https://ms-imaging.org/wp/wp-content/uploads/2016/09/imagingMS.zip is broken http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo is broken

I'm aware that I need to learn more about mass spectrometry, but the initial resources I've found are not making it easy. I plan to delve into your repository to gain a better understanding.

NicoKiaru commented 9 months ago

Hmm, I've found and read a bit the book chapter - it's not going to be easy

NicoKiaru commented 9 months ago

Ok, thanks to your library, I can easily make an ImagePlus for ImageJ. So I'm closing this issue.